ChangeLog.c31
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CHARMM 31 |
| c30a2x |
Evaluation |
February 15, 2003 |
| c31a1 |
Developmental |
August 15, 2003 |
| c31a2 |
Developmental |
February 15, 2004 |
| c31b1 |
Release |
August 15, 2004 |
| c31b2 |
Release |
February 15, 2005 |
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About CHARMM31 Development |
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At the July 2003 CHARMM meeting (The Scripps Research Instutute,
San Diego, California, July 11-13, 2003), we decided to release CHARMM
c30b1 with incorporating enhancements and fixes to the developmental
version c30a2. The modified source code and features are described in
ChangeLog.c30, [3] c30b1 Change Log.
As an on-going project, CHARMM development will be carried out
with CHARMM version 31 series. The c31a1 is developed from the
expanded version c30a2x. The expansion detail is reported below in
the c30a2x Change Log section.
The first distribution version is c30b1 and the first
developmental version is c31a1 in the c31 development lines.
The following describes new features and enhancements incorporated in
the c31 development period.
At the July 2002 CHARMM meeting, we planned to prepare a
c30-expansion and to have it reviewed by Charles L. Brooks, III,
Bernard L. Brooks and Carol B. Post. c30a2x is completed as the
expansion of c30a2.
1.1 Expansion of ID names and Allowed Number of Atoms
Name : Youngdo Won and Bernard R. Brooks
Email Address : won@ihanyang.ac.kr, brb@helix.nih.gov
Institution : National Institute of Health
Date : February 12, 2003
Objectives
----------
CHARMM is expanded to handle upto ten billion atoms and eight
characters for segment ID, residue ID, residue names and atom names.
The expansion is implemented in a conservative way that
(1) Output and file formats are unchanged when CHARMM can warrant
a normal run, i.e. NATOM < 100000, and less than five characters are
used for SEGID, RESID, RES and TYPE.
(2) The number of atoms (NATOM) and the number of characters used in
SEGID, RESID, RES and TYPE are checked when PSF is modified
(created) and when an output is made into a file. Only when
needed, the expanded formats are used.
(3) All previous version data files are accepted. All CHARMM I/O
functions are made backward compatible.
(4) Expanded format files carry a mark (for example, "EXT") that does
not disturb previous version I/O.
(5) The MISCellaneous command "IOFOrmat" may enforce either "OLD format"
or "EXPanded format".
Data File Format
----------------
All data files of the previous versions should be read by the expanded
CHARMM. The normal format data files generated by the expanded CHARMM
should be read by the previous versions.
(1) PSF I/O
Expanded format is marked by "PSF EXT" on the header line. Only
expanded format files carry "EXT", which signals the expanded format
for reading. Expanded format uses I10 atom numbers and
eight-character PSF ID names.
(2) COORdinate Files
Expanded format is marked by "EXT" on the first line after the title
lines where the number of atoms is put. "EXT" indicates the expanded
coordinate file format. All field widths are doubled:
Atom_No Res_No Res_Name Atom_ID X Y Z SEGID RESID W
Normal: I5 I5 1X,A4 1X,A4 3F10.5 1X,A4 1X,A4 F10.5
Expanded: I10 I10 2X,A8 2X,A8 3F20.10 2X,A8 2X,A8 F20.10
(3) SEQUence I/O
Modified to match the expanded coordinate file format.
(4) HBONd, IC, CONStraint, XRAY, IMAGe I/O
Atom numbers use the I10 format and PSF ID names use the A format with
the (1:idleng) width control.
Implementation
--------------
Atom numbers are written in I10 and are read in the free format for
the expanded format I/O. PSF ID names (SEGID, RESID, RES and TYPE)
are written in the "A" format with the width control (1:idleng), where
idleng is set to 4 for normal and 8 for expanded I/O. A PSF ID is
read with the NEXTA8 function.
In psf.fcm
CHARACTER*4 SEGID, RESID, RES, TYPE
is changed to
CHARACTER*8 SEGID, RESID, RES, TYPE
Note that CSTACK is also expanded to CHARACTER*8.
In stream.fcm, three logical QOLDFMT, QNEWFMT, and QEXTFMT and one
integer IDLENG are placed. Defaults are .FALSE. for QOLDFMT and
QNEWFMT and QEXTFMT is determined at the time of I/O request.
QOLDFMT and QNEWFMT are set by the miscellaneous command IOFOrmat and
enforce the normal and the expanded format I/O, respectively. The
command syntax is
IOFOrmat [EXTEnded ]
[NOEXtended]
The format (qextfmt) is determined by calling a logical function
qxform() (util/string.src), which checks if qextfmt is previously set,
if qoldfmt or qnewfmt is set, if NATOM is greater than 100000, and if
any PSFID name is in more than five characters. qxform() should be
called before writing out a file.
I/O of PSFID names are done with the "A" format with (1:idleng). For
example,
WRITE(OUTU,'(A,A)') 'The Segment ID is ',SEGID(ISEG)(1:idleng)
idleng is set to 8 when qextfmt is set (.true.). The default is 4,
for the normal I/O.
Modified Source:
source/adumb/cmds.src, eadumb.src
/cadint/cadini.src
/cff/enbonda_cff.src
/charmm/iniall.src, miscom.src, anacor.src, clustr.src
/correl.src, corrio.src, mantim.src, solana.src
/emap/emapsubs.src
/energy/dmcons.src, ebaspas.src, ediff.src, eintern.src
/enst2.src, epull.src, polar.src
/fcm/cstack.fcm, exfunc.fcm, heappr.fcm, psf.fcm, stream.fcm
/gener/genpsf.src, hbonds.src, mkpres.src, modpsf.src
/psfsum.src, replica.src
/graphics/drawit.src, grutil.src
/gukint/gukini.src
/image/cnbndm.src, images.src, imagio.src, nbondm.src, upimag.src
/io/coorio.src, mainio.src, psfres.src, univio.src
/machdep/quanta.src, space.src
/manip/corman2.src, corman3.src, corman.src, cshake.src, cstran.src
/fsshake.src, hbanal.src, intcor.src, pucker.src, rgyr.src
/rmsdyn.src, scalar.src, shake.src, wrgaus.src
/misc/aspener.src, eef1.src, genetic.src, hbuild.src, mmfp.src
/nmr.src, noe.src, quicka.src, resdist.src, testch.src, xray.src
/mmff/datastruc.src, merckio.src
/molvib/molinp.src, molvio.src, molvsb.src
/nbonds/cnbnd.src, enbonda.src, ewald.src, nbonda.src, nbondg.src
/nbutil.src
/pert/epert.src, icfix.src, icpert.src, tsms.src
/quantum/addlnat.src, qmset.src
/sccdftbint/sccdftbini.src
/shapes/mdlio.src
/solvation/coorman.src, deriv.src, rismio.src, soluu.src
/soluv.src, asolvv.src
/util/array.src, chutil.src, selcta.src, string.src, util.src
/vibran/quasi.src, vibio.src, vibsub.src
Modified Documentation:
doc/miscom.doc, io.doc
Modified Testcase:
test/c24test/pert2.inp ! free format assumes four character names
..............................................................................
1.2 Energy Write Overflow
Name : Youngdo Won
Email Address : won@ihanyang.ac.kr
Institution : Hanyang University
Date : February 13, 2003
printe.src is modified to print large energy values in the assigned
space. The normal format is F13.5, which is adjusted to F13.4, F13.3,
F13.2, F13.1, and E13.5 in order to yield readable numbers. No more
"**********" will be seen in the output.
File Modified:
source/energy/printe.src
The following are introduced and modified during the development period
of February 15, 2002 through August 15, 2002. The developments are
based on two CHARMM versions: c30a2 and c30a2x. Some enhancements and
fixes to c30a2 are also incorporated into c30b1 as described in the
c30b1 release note (ChangeLog.c30) and indicated below.
2.1 TSRI Developments
Name : Wonpil Im, John Karanicolas, Sandeep Patel, Scott Brozell,
Mike Crowley, Charles L. Brooks, III
Email Address : wonpil@scripps.edu , crowley@sripps.edu, brooks@scripps.edu
Institution : The Scripps Research Institute
Date : June 10, 2003
2.1.1. Generalized Born with a simple SWitching (GBSW)
The GBSW module provides the (electrostatic + nonpolar) solvation
energy and forces. A Generalized Born method is used for the
electrostatic part and the solvent-exposed surface ares for the
nonpolar part with a phenomenological surface tension coefficient.
Based on volume integration schemes used in the GBMV module [M.S. Lee,
F.R. Salabury, Jr., and C.L. Brooks III, J. Chem. Phys., 116, 10606
(2002)], we have recast the calculation of the self-electrostatic
solvation energy to utilize a simple smoothing function at the
dielectric boundary. The GBSW model is formulated in this manner to
provide consistency with the Poisson-Boltzmann (PB) theory previously
developed to yield numerically-stable electrostatic solvation forces
based on finite- difference methods [W. Im, D. Beglov, and B. Roux,
Comp. Phys. Comm., 111, 59 (1998)]. However, it is also possible to
mimic the PB results with the molecular surface by reparametrizing two
adjustable parameters, a_0 to modulate the Coulomb field term and a_1
to include a correction term beyond Coulomb field.
The GBSW module takes the influence of biological membranes into
account. Consistent with continuum Poisson-Boltzmann (PB)
electrostatics, the membrane is approximated as an
solvent-inaccessible infinite planar low-dielectric slab. The membrane
GB model closely reproduces the PB electrostatic solvation energy
profile across the membrane.
The GBSW module works with the IMAGE facility. The GBSW
calculations are about 4 times slower than the corresponding vacuum
calculations. Using the simple smoothing function makes the present GB
model roughly 2-3 times faster than the GBMV module.
keyword: GBSW
Files Added:
source/misc/gbsw.src
Files Modified:
install.com
source/charmm/charmm_main.src
/energy/energy.src
New Documentation:
doc/gbsw.doc
New Testcase:
test/c31test/gbsw.test
..............................................................................
2.1.2 Support for usage of a modified van der Waals term
Setting the flag "ETEN" to "ON or OFF" switches the van der Waals to
a modified Lennard-Jones function containing an attractive r^-10 term
and repulsive r^-12 and r^-6 terms. This was introduced to support
simulation of the Go models built by the webserver at
mmtsb.scripps.edu/webservices/gomodel.html
keyword: GOMODEL
Files Modified:
source/charmm/charmm_main.src, iniall.src
/energy/ediff.src, energy.src
/fcm/inbnd.fcm
/manip/corman3.src
/misc/hbuild.src
/nbonds/enbf2.src, enbfast.src, enbond.src, enbonda.src,
/enbondg.src, evdwf.src
/quantum/qmene.src
/util/prpref.src
Modified Documentation:
doc/energy.doc
New Testcases:
test/c31test/eten_1.inp, eten_2.inp
..............................................................................
2.1.3 Polarizable model fluctuating charges (c30b1)
Code for generalized born model added. Works with proteins.
Calling argument list of WRITCV is fixed.
Files added:
toppar/par_all30_cheq_prot.inp, top_all30_cheq_prot.inp
Files Modified:
doc/cheq.doc
source/cheq/fqener.src
/dynamc/dcntrl.src, dynamc4.src, dynamvv.src, nose.src
/fcm/cheqdyn.fcm
/minmiz/steepd.src
/util/prpref.src
New Testcases:
test/c30test/cq1fsvvacu.inp, cq1fsvwat.inp, cqmeohvacu.inp, cqnmawat.inp
/cqtip4pbulk.inp, cq1ab1gbdyn.inp
test/data/top_all30_cheq_prot.inp, 1ab1gbtest.crd, 1fsv_min.crd, cubic.xtl
..............................................................................
2.1.4 Build fixes (c30b1)
IBM platform makefils are fixed and some compile options are set for
platform dependent compilation. Compromise solution to avoid ifc
optimization problems for svdcmp.f and intcor2.f. FC1 is used in
1adumb.mk and manip.mk for compilation, respectively, where ifc FC1 is
set to -O0. stdlib.h is added in socket.c. IBMAIX key is added in
machutil.src. test.com is fixed to run IBM parallel testing.
Files modified:
build/UNX/Makefile_alpha, Makefile_ibmaix, Makefile_ibmaixmp,
/Makefile_ibmsp3
/adumb.mk, manip.mk
source/machdep/socket.c, machutil.src
test/test.com
..............................................................................
2.1.5 GBMV Fixes (c30b1)
New parametrization and bugfixes. Added a guard around a
sequence of assignments in Subroutine RunGBMV1. Removed local
variable R2 and from Subroutine RunGBMVGrid1. Completely removed local
variable RF from Subroutine RunGBMVGrid1.
Files modified:
source/energy/energy.src, gbmv.src, intere.src
/fcm/gbmv.fcm
..............................................................................
2.1.6 Standard coding clean-up (c30b1)
Modified SUBROUTINE GAUSSJ to conform to Charmm coding standards
(fqener.src). PARALLEL code fixes (epath.src). quicksort routine is
moved out of ##IF block for CHEQ (pbeq.src). CHEQ and FASTEW conflict
is terminated with an error message (ewald.src). Some print
statements removed (tsms.src) and variables are initialized (wham.src).
Files modified:
source/cheq/fqener.src
/energy/epath.src
/misc/pbeq.src
/nbonds/ewald.src
/pert/tsms.src, wham.src
..............................................................................
2.1.7 Testcase fixes (c30b1)
fixes for missing parameters (pathint) and to multinode I/O
problems. In molvt6, TOLGrad is set to 0.000002 to attain convergence
on SGI platforms.
Files modified:
test/c26test/pathint.inp
/c27test/gb_mmff94_na-test.inp, gb_mmff94_prot-test.inp
/gb_mmff94_test.inp
/c29test/mctest03.inp, mctest04.inp
/c30test/cftiangl.inp, cftidihe.inp, cftidist.inp, cftmala10.inp,
/cftmtst1.inp, cftmtst2.inp, cftmtst3.inp, cftmtst4.inp
/cftmtst5.inp, molvt6.inp
------------------------------------------------------------------------------
2.2 Cornell University Developments
Name : Guillaume Lamoureux and Benoit Roux
Email Address : Benoit.Roux@med.cornell.edu
Institution : Weill Medical College of Cornell University
Date : June 24, 2003
2.2.1 Dipole correlation and polarizability calculations
In the CORRel command, the MOVIng keyword can be used to compute
the moving average of a time series.
In the VIBRAN command, the DIPOle keyword allows the command to compute
the molecular polarizability. It prints to contribution of each
vibration mode to the polarizability tensor, as well as the total
polarizability. It ignores the rotation and translation modes.
Files Modified:
source/correl/correl.src, anacor.src, mantim.src
/vibran/vibio.src
Modified Documentation:
doc/correl.doc, vibran.doc
..............................................................................
2.2.2 DRUDE command for polarizable force field
The DRUDE command generates a polarizable system by modifying the
topology and parameters of an existing non-polarizable system. For
each selected atom, it creates a "Drude oscillator" by attaching to
the atom an additional particle (using a fictitious chemical bond of
length zero and of force constant 'KDRUDE = k/2'). Each Drude
particle is given a mass and a charge, taken from the mass and the
charge of its atom (so that the total mass and charge are conserved
for the "atom-Drude" pair).
Note: The calling syntax of the CODES subroutine is changed.
Files Added:
source/gener/drude.src
Files Modified:
source/fcm/psf.fcm, ssbp.fcm
/cff/ewald_cff.src
/charmm/charmm_main.src, iniall.src
/correl/correl.src
/dynamc/trnphi.src
/energy/energy.src
/gener/genpsf.src, psfsum.src, update.src
/manip/shake.src
/misc/hbuild.src, ssbp.src
/mmff/enbfast_mm.src, enbscalar_mm.src
/nbonds/ewald.src, evdwf.src, ewaldf2.src
/pert/pert.src, epert.src
/quantum/qmset.src
New Documentation:
doc/drude.doc
New Testcases:
test/c31test/drude_benzene.inp, swm4.inp
..............................................................................
2.2.3 TPCONTROL and extended dynamics
The TPCONTROL command specifies the thermodynamic ensemble to be
simulated with "DYNA VV2", using extended dynamics: Nose-Hoover
equations for constant volume and constant temperature (the NVT
ensemble) and Anderson-Hoover equations for constant pressure and
temperature (the NPT ensemble). It allows multiple thermostats.
"DYNA VV2" is a velocity-Verlet algorithm created to simulate
efficiently the motion of Drude oscillators (created by the DRUDE
command), and it understand the special nature of the Drude
oscillators.
Note: The calling syntaxes of the subroutines WRIDYN and READYN are
changed.
Files Added:
source/dynamc/tpcontrol.src, dynamvv2.src
Files Modified:
source/fcm/nose.fcm
/dynamc/dcntrl.src, dynio.src, dynamc.src
/io/coorio.src
/mbond/mbback.src
/mc/mcio.src
New/Modified Documentation:
doc/tpcontrol.doc, dynamc.doc
New Testcase:
test/c31test/swm4_liquid.inp
..............................................................................
2.2.4 Ambiguously selectable NOE restraints
It is often useful to apply a distance restraint between several
groups of atoms, not knowing in advance which pair of atoms must be
explicitly selected. For example, this happends often when
restraints are implemented in a symmetric dimer and one does not
know whether a distance restraint is intra or inter molecular. With
the key word MINDIST it is now possible to apply such restraint in the
NOE module.
Files Modified:
source/fcm/noe.fcm
/energy/energy.src
/misc/noe.src
/pert/epert.src
Modified Documentation:
doc/cons.doc
..............................................................................
2.2.5 The RMSD constraint bugfix
The rmsd energy constraint as called on each node with MPI. The
call to ECNST3 in ecnstr.src is now protected with a "IF(MYNOD.EQ.0)"
to be called only once. This is a quick fix for now. A better
parallelization of the CONS RMSD could be done in the near future.
The passing variables in the call to ECNST3 are corrected.
Files involved:
source/energy/ecnstr.src
------------------------------------------------------------------------------
2.3 Developments at University of Vienna
Name : Tibor Rudas, Martin Leitgeb, Stefan Boresch, and
Othmar Steinhauser
Email Address : tibi@mdy.univie.ac.at, martin@mdy.univie.ac.at, and
stefan@mdy.univie.ac.at
Institution : Molecular Dynamics and Biomolecular Simulation group
at the Department of Theoretical Chemistry and
Molecular Structural Biology, University of Vienna
Date : June 13, 2003
2.3.1 Solvent shell decomposition
SHELL decomposes (selected) solvent residues (atoms) into shells
based on the distances from (a selected set of) solute atoms. The
distance calculation is done by a cubing algorithm (adapted from
images/nbndgcm.src by M. Crowley). [The functionality could be
duplicated by the trajectory reader and carefully chosen SELEct
statements, but the present code is orders of magnitude faster]
SHELL can use crystal/images to handle correctly
coordinates/trajectories which were generated using periodic boundary
conditions with all boxtypes.
Lists of atoms in the individual shells, as well as those in the bulk
are generated for use in calculations by other modules (e.g. CORREL).
Two series using the shell decomposition - SDIP and SATM - are
available in CORREL if the SHELL keyword is present in pref.dat
(described along with two other new timeseries in CORREL, which
were submitted separately).
All relevant code is encapsulated by a new keyword - SHELL - so this
feature can be safely deactivated.
Files Added:
source/correl/shell.src, shlsel.src
/fcm/shell.fcm
Files Modified:
source/charmm/charmm_main.src, iniall.src
New Documentation:
doc/shell.doc
New Testcase:
test/c31test/shell.inp
..............................................................................
2.3.2 New CORREL time series
Correl has been augmented by the following four time series
DIPO - dipole moment of (statically) selected atoms (e.g., the
dipole moment of a protein or of all waters)
SDIP - dipole moment of a water (solvent) shell.
(Requires the SHELL module submitted separately. Needs the
keyword SHELL to be set in pref.dat)
SATM - a true/false (0/1) timeseries if a given atom is in a certain
shell (also only available if SHELL is present in pref.dat)
VECM - an image-aware analogue to VECT XYZ. Combined with an
appropriately chosen CUTIM (see doc.) the vector between the
two atoms always represents the minimum image distance.
Since two of the series (SDIP and VECM) can/must use images, ANACOR
(filling the series from a trajectory) was modified to update images
after each frame is read).
SDIP and SATM are encapsulated by ##IF SHELL -- ##ENDIF blocks since
they can only be used together with the SHELL module. Detailed
description of these series is thus also included into shell.doc.
Files Modified:
source/correl/correl.src, anacor.src
Modified Documentation:
doc/correl.doc
Modified Testcase:
test/c31test/cortst2.inp
..............................................................................
2.3.3 Efficient radial distribution function
RDFSOL computes radial distribution functions (e.g. g_oo, g_oh and
g_hh), as well as some related functions (e.g. the dipole-dipole
correlation function). Some of the functions provided can also be
calculated by COOR ANALYSIS (solana). The improvements of RDFSOL are
twofold:
(i) It uses crystal/image instead of calculating minimum distances
directly; thus it supports periodic boundary conditions for all
boxtypes.
(ii) The distance calculations can be done using a cubing algorithm
(adapted from images/nbndgcm.src by M. Crowley). While this
has a certain performance penalty for small systems, it
drastically speeds up calculations for large systems in some
cases compared with COOR ANAL.
A user function (USRRDF) as fill-function is implemented to enable
easy addition of new functions of interest.
The complete code is surrounded by a ##IF RDFSOL -- ##ENDIF block to make
its compilation optional.
Files Added:
source/correl/rdfsol.src, rdfsl2.src, shlsel.src
Files Modified:
source/charmm/charmm_main.src, iniall.src
New Documentation:
doc/rdfsol.doc
New Testcases:
test/c31test/rdfsol.inp, rdfsol2.inp
..............................................................................
2.3.4 MMFP GEO restraints in alchemical PERT simulations
Presently, the MMFP energy terms are supported by the PERT module
only as an invariable energy term, and cannot be part of the
alchemical transformation itself. The proposed modification makes
MFF-potentials modifiable in PERT free energy simulations.
To avoid the overhead of computing GEO restraints twice in situations
where they are not part of the alchemical mutation, the new code is
only activated if the MMFP keyword is given in the initial PERT statement
(see documentation for details). Following PERT MMFP
all variables and arrays needed for the specification of the
MFF-potentials are duplicated in pert.src.
The GEO energy routines are now called twice, once in the lambda = 0 section
and once in the lambda = 1 section.
Again, existing PERT scripts using GEO restraints as constant
energy terms behave as before and should not experience any performance
penalty!
Files Modified:
source/pert/pert.src, epert.src
/fcm/pert.fcm
/charmm/iniall.src
Modified Documentation:
doc/pert.doc
New Testcase:
test/c31test/pert-mmfp.inp
..............................................................................
2.3.5 Exponential flat bottom "Saxon-Wood" potential
We have implemented an additional restraint for MMFP based on the
Saxon-Wood potential (developed originally in nuclear physics). This
potential consists of an almost flat region (of variable width) about
the reference value (here the system is practically undisturbed),
which is confined by exponentially rising walls, whose height can also
be controlled. Thus, the system is restricted very effectively to a
predefined region of the phase space. (The potential is similar to a
flat-bottom harmonic well, but it is completely smooth and has walls
of finite height.
The restraining potential was implemented in the MMFP module (see the
CHARMM code in mmfp.src) by using existing data structures. Aside from
the new keyword SAWO, which must be added in the input script after
the GEO command, no additional variables had to be introduced. All
existing parameters, which determine the shape, distance and force
constant of the restraints, have the usual meaning for the new
potential. This type of potential should facilitate applications like
binding free energy difference calculations.
Files Modified:
source/misc/mmfp.src
Modified Documentation:
doc/mmfp.doc
New Testcase:
test/c31test/sawo.inp
------------------------------------------------------------------------------
2.4 UC-Berkeley Developments
Name : Aaron R. Dinner
Email Address : ardinner@uclink.berkeley.edu
Institution : University of California, Berkeley
Date : July 3, 2003
2.4.1 Grand canonical Monte Carlo
A relatively rudimentary grand canonical Monte Carlo (GCMC) scheme
was implemented through the SCALAR, MOVE and MC commands. Note that
this code is considered developmental and thus subject to change
without backward compatibility.
Grand canonical atoms are designated as active through the GCMCon
array, which can be manipulated with the SCALAR command. A value
of 1 indicates that an atom is active and a value of 0 indicates
that an atom is inactive. It is suggested that there be roughly twice
as many grand canonical molecules as anticipated will be active on
average to accomodate fluctuations.
Atoms that block grand canonical insertions in the cavity-based
schemes described below are also initialized through a SCALAR array,
GCBLocker. A value of 1 indicates that an atom is a blocker, and
a value value of 0 indicates that it is not. Time can be saved by
excluding hydrogens.
Grand canonical moves are declared through MOVE ADD MVTP GCMC.
Translation and rotation moves of these molecules should be linked
to the GCMC move group to avoid wasting time moving inactive atoms.
Two algorithms for facilitating insertions at high density/confinement
can be used. The cavity bias method [M. Mezei, Mol. Phys. 40, 901 (1980)]
generates a set of candidate insertion positions at each GCMC step randomly,
determines the ratio P_N = cavity sites/total sites, and picks a cavity site
for insertion. The acceptance probability is adjusted based on the average
of P_N to satisfy detailed balance. Simple cavity bias is used if NGCTry is
greater than 0.
Grid insertion is an improvement of the random cavity bias [M. Mezei, Mol.
Phys. 61, 565, (1987)], and works by maintaining a dynamic grid variable
within the GCMC volume specifying the cavity sites. It is more memory
intensive and slower at lower density, but generally more efficient at
higher density and confined geometry such as within the binding pocket
of a protein. Grid-based cavity bias is used if RGRId is greater than 0.
As indicated above, the insertion volume can be either spherical or
rectangular.
Current limitations (other than those normally associated with MC):
1. Only atom-based non-bonded lists can be used.
2. The trajectory saved contains all of the grand canonical molecules.
The inactive coordinates are set to -9999.9d0 before being written.
When using the trajectory file, read the trajectory and then delete the
inactive molecules: "DELEte atoms select .byres. prop X .lt. -999.0 end".
3. In grid-based simulations, the grid is updated during non-GC moves using
the assumption that all moves translate and rotate species of size
comparable to the grand canonical molecules. If you are using
grid-based GCMC, with a macromolecular solute, don't allow the
solute atoms to move during the GCMC.
Files Added:
source/fcm/gcmc.fcm
/mc/mvgcmc.src
/misc/distrib.src
Files Modified:
source/fcm/mc.fcm
/charmm/iniall.src
/manip/scalar.src
/mc/mc.src, mcener.src, mcimge.src, mcio.src, movead.src,
/moveln.src, mvrtrn.src
/nbonds/enbfast.src
/util/selcta.src
..............................................................................
2.4.2 Momentum-enhanced Hybrid Monte Carlo
The method is described in Andricioeai, I., Dinner, A. R.
and Karplus, M. (2003) Self-guided enhanced sampling methods
for thermodynamic averages. J. Chem. Phys. 118, 1074-1084.
The code is encapsulated by the MEHMC keyword in pref.dat.
Files Added:
source/fcm/mehmc.fcm
Files Modified:
source/dynamc/dynamc.src
/mc/movead.src, mvhmc.src, mc.src
..............................................................................
2.4.3 Transition Path Sampling
The Transition Path Sampling (TPS) methods introduced by Chandler and
co-workers to sample rare events (see tps.doc) are implemented as
extensions of the RXNCoor, DYNAmics, and USER commands in CHARMM. The
TPS keyword must be included in pref.dat for the code to be compiled.
The code uses the DYNAMC integrator (either leapforg Verlet or Langevin).
Files Added:
source/dynamc/tps.src
Files Modified:
source/dynamc/dcntrl.src, dynamc.src
/rxncor/rxndef.src, rxnene.src
/fcm/rxncom.fcm
New Documentation:
doc/tps.doc
New Testcase:
test/c31test/tps_leap.inp
------------------------------------------------------------------------------
2.5 TReK (version 2.10), a new implementation of CPR
Name : Stefan Fischer
Email Address : stefan.fischer@iwr.uni-heidelberg.de
Date : July 5, 2003
The program TReK (Trajectory REfinement & Kinematics)
is a new implementation of a collection of tools for finding the
minimum-energy path that joins two known structures representing
the reactant and the product states of a reaction.
It has been interfaced with CHARMM. The functionality of TReK
encompasses and goes beyond that of the old TRAVel module.
An effort was made to reproduce the "look & feel" of
TRAVEL, whose input-scripts should work with TReK.
The main tool is the CPR (Conjugate Peak Refinement) algorithm, which
refines an initial guess of the path and finds all the saddle-points.
Other tools include the SCM (Synchronous Chain Minimization) algorithm
and the SDP (Steepest Descent Path) method, which both allow to smooth
a path whose saddle-points are already known.
The purpose of the new design of TReK (and main improvement
relative to TRAVel) is :
- to allow the refinement of long transition paths with hundreds of
saddle-points in very large molecules with several thousand atoms.
- improved efficiency and robustness for use with quantum potentials.
Some of the new features are :
1) Much more user-friendly documentation (./doc/trek.doc).
2) TReK is now parallelized. It scales as well as MD.
It was tested under Linux LAM-MPI and MPICH libraries, and under
SGI's system MPI libraries.
3) The numerical robustness of the various algorithms has been
much improved.
4) An important improvement is the way CPR searches
a path for energy-maxima. In TRAVel, a constant step-size was
used to scan the whole path and was reduced until it was small
enough to adequately probe the most complex region of the energy
surface underlying the path. This was inefficient, since the
smallest step was used everywhere along the path, resulting in
more energy-calls than necessary.
In TReK, the step-size varies along the path and automatically
adapts to the topography of the energy surface. This is more
efficient and makes CPR more robust by preventing the infinite
looping that can occur when the step-size is not small enough.
5) CPR writes a restart-file when a path is saved.
When the CPR-calculation is continued, this file serves two purposes :
- Flagging those path-points that have already been identified
as saddle-points, so that they don't have to be flagged manually
each time a new TReK session is started.
- Saving CPU-time by storing the energy-profile along the path,
avoiding the initial energy-scan of the whole path when
continuing a CPR refinement in a new TReK session.
6) When the initial guess for a path is very poor or some of its
points are very strained, some atoms can experience excessive
forces, so that they would get displaced too much during
the optimization of the path-points. This is prevented by limiting
the rate of displacement to some maximum tolerated value.
7) The energy surface can be expressed in terms of the mass-weighted
coordinates, which allows to find the so-called "intrinsic" path.
8) The tool for removing points from a path ("TRAJ DECRease")
now can preserve saddle-points and local minima along the path and
does not introduce energy peaks. This allows to delete superfluous
path-points, saving CPU-time when smoothing the path with SCM.
Files Added:
source/fcm/trek1.fcm, trek2.fcm
Files Removed:
doc/travel.doc
Files Modified:
source/fcm/travel.fcm
/rxncor/adiab.src, travel.src, travel2.src
/charmm/charmm_main.src
New/Modified Documentation:
doc/trek.doc, parallel.doc
------------------------------------------------------------------------------
2.6 Developments at University of Kansas
Name : Krzysztof Kuczera
Email Address : kkuczera@ku.edu
Institution : University of Kansas
Date : June 11, 2003
2.6.1 MOLVIB module bug fix and upgrade (c30b1)
Eliminated bugs caused by (a) conversion to FORTRAN77 and (b) hidden
fixed dimension in routine MATNV. Changed PED to allow systems with above 99
coordinates. Modified array IO to simplify running test cases.
Files Modified:
source/molvib/molvco.src, molvib.src, gfdiag.src
/molvut.src, molvio.src, molvsb.src
New test cases:
test/c30test/molvt1.inp, molvt2.inp, molvt3.inp, molvt4.inp,
/molvt5.inp, molvt6.inp, molvt7.inp
..............................................................................
2.6.2 Conformational free energy thermodynamic integration (c30b1)
Test cases and description are expanded for conformational free energy
thermodynamic integration (part of TSM module).
Files Modified:
doc/cfti.doc
Files Removed:
test/c26test/cftigas.inp, cftmgas.inp
New test cases:
test/c30test/cftidist.inp, cftiangl.inp, cftidihe.inp, cftmala10.inp,
/cftmtst1.inp, cftmtst2.inp, cftmtst3.inp, cftmtst4.inp,
/cftmtst5.inp
------------------------------------------------------------------------------
2.7 Mechanical pulling of two atoms (AFM)
Name : Emanuele Paci
Email Address : paci@bioc.unizh.ch
Institution : University of Zurich
Date : June 17, 2003
AFM is an external perturbation designed to pull macromolecules
mimicking single molecule experiments (AFM or LOT). There are three
possible way of simulating the pulling; all consist in applying a
suitable force to two atoms. The force is identical in magnitude for
the two atoms, parallel to the two atoms and directed in the direction
of increasing distance. The difference in the forces applied concerns
their dependence on the time. The three methods currently implemented
are: 1) constant force, 2) steered molecular dynamics, 3) biased
molecular dynamics (see HQBM.DOC).
Files Added:
source/fcm/afm.fcm
/energy/afm.src
Files Modified:
source/charmm/charmm_main.src
/energy/energy.src, eutil.src
/fcm/energy.fcm
Added Documentation:
doc/afm.doc
Added Testcase:
test/c31test/afm.inp
------------------------------------------------------------------------------
2.8 GAMESS-UK Interface Updated (c30b1)
Name : Paul Sherwood
Email Address : p.sherwood@daresbury.ac.uk
Institution : CLRC Daresbury Lab.
Date : July 1, 2003
Fix for the special case of Gaussian blur with wmain=0.0 (should
implement a point charge but the last version did not).
Changes to GAMESS-UK build procedure for use with CHARMM are
added to install.com. Integer*8 build is needed for compatibility
with some GAMESS-UK builds so this is now supported by install.com
(was previously available for GNUALPHA only). This was partially
implemented in a previous checking but is complete now.
Files Modified:
install.com
build/UNX/Makefile_alpha
source/gukint/gukini.src
/machdep/paral3.src
/gamint/ddi.src
/cadint/cadini.src
/flucq/fluqqmmm.src
/machdep/space.src
/util/util.src, datstr.src
------------------------------------------------------------------------------
2.9 SUN64 port for running on 64-bit Solaris (c30b1)
Name : Bogdan Costescu
Email Address : bogdan.costescu@iwr.uni-heidelberg.de
Institution : IWR, University of Heidelberg
Date : June 6, 2003
Add SUN64 port which allows using 64-bit file access and memory
allocations on 64-bit Solaris. A new keyword (SUN64) is introduced to
allow code changes with respect to the SUN port; SUN64 is to be used
in addition to the SUN keyword. To compile, something like the
following line should be used:
./install.com sun64 medium FULL
Usage of the "64" install switch is not supported, so the following line is
not valid:
./install.com sun medium FULL 64
To avoid breaking output format for other ports, printing of heap-related
64-bit values which do not fit in the existing integer field width is
protected by "##IF SUN64".
Files Added:
build/UNX/Makefile_sun64
Files Modified:
install.com
source/machdep/machutil.src, space.src
/solvation/fft.src
/util/util.src
------------------------------------------------------------------------------
2.10 Developments at NIC-Slovenia
Names : Milan Hodoscek
Email Address : milan@cmm.ki.si
Institution : National Institutes of Chemstry, Ljubljana, Slovenia
Date : July 7, 2003
2.10.1 Parallelization of GRAPE interface in CHARMM
GRAPE interface in CHARMM was parallelized for more efficient
use of a large number of GRAPE boards.
Files Modified:
doc/parallel.doc, nbonds.doc
source/fcm/grape.fcm
/nbonds/grape.src
..............................................................................
2.10.2 Support for new version of GAMESS
Newest GAMESS version 14 JAN 2003 (R2) is supported in CHARMM
Files Modified:
source/gamint/gamess/{gamess.src,gmsnbo.src,grd1.src,grd2a.src,
guess.src,inputa.src,inputb.src,inputc.src,
int1.src,iolib.src,mccas.src,prplib.src,
prppop.src,rhfuhf.src,scflib.src,
unport.src,zunix.c}
..............................................................................
2.10.3 Support for many non-interacting QM regions within QM/MM system
The interface of GAMESS/CHARMM was extended to support the calculations
of many QM regions withing QM/MM system which don't interact. The
method is extension of the OLAP command in CHARMM to allow for
flexible structural alignement of systems with unknown parameters and
other docking problems.
Files Modified:
source/charmm/iniall.src
/fcm/gamess.fcm
/gukint/gukini.src
doc/gamess.doc
..............................................................................
2.10.4 Code cleanups and compiler bugs (c30b1)
Some bugfixes for compiler, and minor modifications
Files Modified:
source/charmm/charmm_main.src
/fcm/dimens.fcm (more realistic formula for MAXT&MAXP)
/gener/update.src
/machdep/socket.c
/misc/olap.src
/nbonds/nbonda.src, nbonds.src
/quantum/addlnat.src
/sccdftbint/sccdftbini.src
/util/array.src
------------------------------------------------------------------------------
2.11 Developments at the National Institute of Health
Name : Jhih-Wei Chu, Bernhardt Trout and Bernard R. Brooks
Email Address : trout@mit.edu, brbrooks@helix.nih.gov
Institution : Department of Chemical Engeeniring, MIT;
Laboratory of Biophysical Chemistry, NHLBI, NIH
Date : July 7, 2003
2.11.1 Nudged elastic bend (NEB) with ABNR support
The new Nudged Elastic Bend (NEB) method was developed within
RPATH which supports ABNR minimizer.
New files:
source/fcm/pderiv.fcm, neb.fcm
test/c31test/nebdiala.inp, nebdialapmf.inp
Files modified:
source/charmm/iniall.src
/energy/ecnstr.src, energy.src, epath.src
/fcm/path.fcm
/minmiz/abner.src, egrad1.src, steepd.src
/gukint/gukini.src
..............................................................................
2.11.2 Flexible parameter reader
The FLEX keyword in READ PARAM command specifies the new flexible
parameter format.
READ { PARAmeter { CARD [PRINt] [APPEnd] [FLEX] } }
{ { [FILE] [NBON ] [MMFF] } }
This is the same as the standard CHARMM parameter format, but;
(1) allows general wildcarding for all terms
(2) allows parameter substitution for missing paramters
(3) does not require a previously read RTF (no global MASSES list required)
(4) allows the definition of paramter equivalence groups.
New testcase files:
test/c31test/flexpartest.inp
/data/flexpartest.prm, flexpartest_h.prm, flexpartest_xh.prm
Files modified:
doc/io.doc
source/charmm/iniall.src
/correl/correl.src
/dynamc/trnphi.src
/fcm/deflts.fcm, param.fcm
/gener/genpsf.src, hbonds.src, update.src
/image/upimag.src
/io/mainio.src, parmio.src
/manip/shake.src
/misc/hbuild.src
/pert/pert.src
/quantum/qmset.src
..............................................................................
2.11.3 QUICK command overhauled
The quick command has been extended and improved. The following
new features;
(1) Support for both "old" and "new" syntax (##QUICK_SELECT is removed)
(2) Projects positions onto defined AXIS (from COOR AXIS command)
(3) Allows the use of comparison coordinates for any specified atom
(4) Allows the use of a center of mass/geometry for a group of atoms
(5) Allows more ways to select specific atoms.
Files modified:
source/misc/quicka.src
..............................................................................
2.11.4 Ehancements and Fixes
(1) Codes for RMS best fit, CRYSTAL commands, and AXIS commands are
improved. Error processing is improved in PERT. A PME bug is fixed
in pme.src. Changed the default for Ewald net charge correction
(nbonds/nbutil.src). ATOMID call is fixed in manip/cstran.src.
Calling argument lists are checked (LISCHECK) and fixed (done on the
prerlease version c31a0).
(2) prefx.f (prefx.src) is improved to incorporate preprocessing
keywords (specified in pref.dat) into the code compiled.
(3) SGLD (Self-Guided Langevin Dynamics) feature is separated into
dynamc/sglds.src and fcm/sgld.fcm (new documentation is doc/sgld.doc).
(4) CMAP code is separated into energy/ecmap.src
(5) Hugh memory resiedent arrys are moved into HEAP (polar.src)
(6) Source file format is fixed to follow the guideline below.
- The last end statement in src files must be in upper case: END.
Needed for some legacy compilers.
- ##IF construct are grouped with comments in parentheses, e.g.,
##IF (pert_code)
....
....
##ELSE (pert_code)
....
....
##ENDIF (pert_code)
- ## keyward usage fixed: !##.not. is used instead of !##.NOT. and !##IF is
not allowed (though it works).
- Unused ## keys are removed (in progress) : OPLS, QUICK_SELECT and
others.
(7) documentation updated.
New Files:
doc/sgld.doc, preflx_list.doc
source/dynamc/sglds.src
/energy/ecmap.src
/fcm/sgld.fcm
test/c31test/sgld.inp
Files removed:
source/dynamc/meanf.src
/fcm/fbias.fcm
Files modified:
doc/corman.doc, crystal.doc, developer.doc, dynamc.doc, io.doc,
/lonepair.doc, minmiz.doc, miscom.doc, nbonds.doc, perturb.doc,
/subst.doc
source/adumb/cmds.src, eadumb.src, svdcmp.src
/charmm/iniall.src
/cheq/fqcom.src, fqener.src, fqminut.src
/correl/clustr.src, rdfsl2.src, rdfsol.src, shell.src, solana.src
/dynamc/dcntrl.src, dynamc4.src, dynamc.src, dynamcv.src,
/dynamln.src, dynamvv2.src, dynamvv.src, dynsub.src, dynio.src,
/tpcontrol.src, tps,src, trnphi.src, tmd.src
/emap/emapio.c, emapsubs.src
/energy/cenerf.src, ebaspas.src, ecnstr.src, epath.src, eintern.src
/gbmv.src, printe.src, polar.src, rgy.src, rmsd.src
/fcm/afm.src, cff.fcm, cheqdyn.fcm, clcg.fcm, cnst.fcm,
/consta.fcm, derivq.fcm, eef1.fcm, emap.fcm,
/excl.fcm, exfunc.fcm, flucq.fcm, gamess.fcm,
/gbmv.fcm, gbsw.fcm, gcmc.fcm, genborn.fcm, lambda.fcm,
/leps.fcm, lobos.fcm, mbmts1.fcm, mbmts.fcm, mbond.fcm,
/mbpar.fcm, mbspp.fcm, mc.fcm, mehmc.fcm, mltcanon.fcm,
/olap.fcm, path.fcm, pathint.fcm, pert.fcm, rtf.fcm,
/rwlamb.fcm, sasa.fcm, sccdftb.fcm, spacod.fcm, spapar.fcm,
/traj.fcm, travel.fcm, tsmh.fcm, tsms.fcm, umb.fcm
/gamint/ddi.src
/gener/drude.src, mkpres.src, modpsf.src, update.src
/graphics/graphx.src
/gukint/gukini.src
/image/cnbndm.src, nbndgcm.src, crystal.src, pbound.src
/io/coorio.src, psfres.src, rtfio.src, trajio.src, univio.src
/machdep/paral1.src, corman.src
/manip/corman2.src, corman3.src, cshake.src, cstran.src,
/dynanal.src, hbanal.src, helix.src, rmsdyn.src,
/rotlsq.src, scalar.src
/mbond/mbback.src, modtrans.src
/mc/mcener.src, mcio.src, mcmini.src, moveln.src
/minmiz/abner.src, conjug.src, egrad1.src, minmiz.src,
/nraph.src, powell.src, steepd.src, tndriv.src
/misc/aspener.src, distrib.src, genetic.src, nmr.src, xray.src
/mmff/merckio.src
/nbonds/enbf2.src, enbfast.src, enbondg.src, enbond.src,
/evdwf.src, grape.src, nbutil.src, pme.src, pmeutil.src
/pert/block.src, epert.src, pert.src, puic.src, tsms.src
/quantum/addlnat.src
/rxncor/adiab.src, lupopt.src, rxndef.src, rxnene.src,
/travel2.src
/solvation/rismio.src
/util/clcg.src, imsl.src, prpref.src, selcta.src, string.src
/vibran/quasi.src, rbquas.src, vibio.src
tool/prefx.f, prefx.src
------------------------------------------------------------------------------
2.12 HEAP allocation and release status information
Name : Youngdo Won
Email Address : won@sulu.hanyang.ac.kr
Institution : Hanynag University and NIH
Date : April 25, 2003
An array is allocated on the heap by the ALLHP function and is
released by the FREHP subroutine. Upon allocating/releasing the heap
space, it is nice to print the information on the dynamic heap usage.
When the heap-print-out option is set (by the TEST HEAP command),
(1) the ALLHP function is modified to print the message:
ALLHP> <src/routine> allocates <words> words from <address> for <variable>
(2) the FREHP subroutine is modified to print the message:
FREHP> <src/routine> releases <words> words of <variable> at <address>
The calling argument list of ALLHP and FREHP is modified to add
<src_file_name>, <routine_name>, and <variable_name>, for example,
HPNDIS = ALLHP(IREAL8(NDISTA),'cmds.src','UMBAN2','HPNDIS')
CALL FREHP(HPNIDS,IREAL8(NDISTA),'cmds.src','UMBAN2','HPNDIS')
ALLHP and FREHP of util/util.src are modified to put the information
printing when PRHEAP is set.
Note that the calling argument list of ALLHP and FREHP is changed.
Files Modified: (142 source files)
adumb/cmds.src, umb.src
charmm/charmm_main.src, iniall.src
cheq/fqener.src
correl/correl.src, solana.src
dimb/dimbutil.src, nmdimb.src
dynamc/dcntrl.src, nose.src, tmd.src
emap/emapsubs.src
energy/dmcons.src, ecnstr.src, ecntrl.src, ediff.src, enefvp.src,
/energy.src, eolap.src, epath.src, epull.src, gbmv.src, genborn.src,
/intere.src, pathint.src, rgy.src, rmsd.src
flucq/flucq.src, fluqqmmm.src
gener/genpsf.src, makphi.src, modpsf.src
graphics/graphx.src
image/crystal.src, eimage.src, images.src, imnbfp.src, nbndgcm.src,
/upimag.src, xtlfrq.src
io/coorio.src, parmio.src, trajio.src
machdep/paral1.src
manip/corman2.src, corman3.src, corman.src, cshake.src, cstran.src,
/fsshake.src, hbanal.src, intcor.src, rmsdyn.src, scalar.src
mbond/mbmts.src
mc/mcace.src, mcener.src, mcimge.src, mcio.src, mcmini.src, mc.src,
/movead.src, moveio.src, moveln.src, mvcrot.src, mvdihe.src, mvhmc.src,
/mvrtrn.src
minmiz/abner.src, egrad1.src, nraph.src, powell.src, steepd.src, tndriv.src
misc/eef1.src, genetic.src, grid.src, gsbp2.src, gsbp.src, mmfp.src,
/nmr.src, olap.src, pbeq2.src, pbeq.src, primsh.src, resdist.src,
/sasini.src, ssbp.src, surfac.src, testch.src, zmat.src
mmff/efast_mm.src, enbfast_mm.src
molvib/molvco.src
nbonds/enbond.src, etable.src, evdwf.src, ewaldf2.src, ewaldf.src,
/fma.src, nbexcl.src, nbndcc.src, nbndfp.src, nbndgc.src, nbonds.src,
/nbutil.src, pme.src, pmeutil.src
pert/block.src, epert.src, icfcnf.src, icpert.src, pert.src, puic.src,
/tsme.src, tsms.src, wham.src
quantum/qmene.src, qmjunc.src, qmnbnd.src, qmset.src
rxncor/adiab.src, lupopt.src, path.src, rxndef.src, travel2.src, travel.src
shapes/eshape.src, shapes.src
solvation/cycles.src, deriv.src, rism.src, solvation.src
util/datstr.src, pointer.src, selcta.src, util.src
vibran/vibio.src, vibran.src, vibsub.src, vibutil.src
The following are introduced and modified during the development period
of August 15, 2003 through February 15, 2004.
3.1 TSRI Developments
Name : Sandeep Patel, Jainhan Chen, Scott Brozell, Mike Crowley,
Charles L. Brooks, III
Email Address : sandeep@scripps.edu, jainhan@scripps.edu,
crowley@sripps.edu, brooks@scripps.edu
Institution : The Scripps Research Institute
Date : December 29, 2003
3.1.1 Charge Equilibration Polarizability Enhancements and Fixes
Allocate heap space for wall potential and charge mass arrays if CHEQ
requested. Removed unnecessary comments and variables in various routines.
Fixed routine GAUSSJ in cheq/fqener.src (declaration of variable PIVINV).
Files Modified:
source/charmm/charmm_main.src, iniall.src
/cheq/fqcom.src, fqener.src
/dynamc/dynamc.src, dynamvv.src
/energy/energy.src
/fcm/cheqdyn.fcm
/mbond/mbback.src
..............................................................................
3.1.2 NOE Potential with Soft Asymptote
Implementation of a soft-square NOE potential where the square-well
function is used for distances within a specified "switching" region
(specified by RSWIitch keyword) and outside this region a "soft"
asymptote is used:
/ 0.5*KMIN*(RAVE-RMIN)**2 R<=RMIN
E(NOE) = | 0.0 RMIN RMAX+RSWITCH
In addition, an option (invoked by SUMR) of using summation instead
of averaging for calcuating R was added:
R = [ Sum_ij ( Rij**(1/REXP) ) ]**REXP
Files Modified:
source/adumb/cmds.src, eadumb.src
/energy/energy.src
/fcm/noe.fcm, pert.fcm, umb.fcm
/mc/mcener.src, netic.src
/misc/noe.src
/pert/epert.src
Modified Documentation:
doc/cons.doc
..............................................................................
3.1.3 Endian-checking Trajectory Reader
Reads trajectories transparently to the user regardless of whether it
is big or little endian. Saves having to do dyna format and dyna unformat
on large trajectories that come from machines with opposite endianness.
NOTE: This automatic file conversion does not yet work properly on IA64
architectures, will be fixed soon.
Files Modified:
source/dynamc/dynio.src, dynsub.src
/fcm/iochan.fcm
/machdep/cstuff.c, machio.src
/util/title.src
New Testcase:
test/c31test/endian.inp
/data/endian_0.crd, endian_1.crd
..............................................................................
3.1.4 Intel 64 bit Machine Ports
Added support for new machine architecture and compilers. The new
install.com keys and switches are
hpitanium for HP-UX Itaniums
altix for SGI Altix series (64 bit)
gnu EFC for efc intel 64 bit compiler
Roberto Gomperts added mpi8 routines. These convert 8 byte integer
arguments for charmm built with I8 into 4 byte integer arguments for
mpi calls and are guarded by the pref keyword ALTIX_MPI which is
activated by the install.com target altix. This mechanism enables
coexistence with other mpi implementations, such as LAM, that do not
support MPI_INTEGER8.
Modified to build 64 bit on Linux Itaniums using install keyword EFC.
Roberto Gomperts identified some mpi_allreduce calls that were not
passing the correct message lengths for 64 bit integers.
A general solution would be to use MPI_INTEGER8, but that is not
supported by all mpi implementations yet. So the message count is
doubled.
Files Added:
build/UNX/Makefile_altix, Makefile_hpitanium
Files Modified:
install.com
build/UNX/Makefile_gnu
source/correl/solana.src
/energy/gbsw.src
/fcm/impnon.fcm
/machdep/machio.src, machutil.src, paral1.src, paral2.src
/space.src, startup.src
/manip/shake.src
/nbonds/pmeutil.src
..............................................................................
3.1.5 McIntosh OSX Port
Port added for for Macintosh OSX. The install.com target is set to OSX
and the compiler switch is either xlf or g77. The pref.dat keywork is OSX.
install.com osx [ xlf | g77 ]
Files Added:
build/UNX/Makefile_osx
Files Modified:
install.com
build/UNX/misc.mk, solvation.mk
source/cadint/cadini.src
/correl/solana.src
/emap/emapio.c
/fcm/impnon.fcm
/machdep/cstuff.c, machio.src, machutil.src, paral1.src
/paral2.src, parset.src, space.src, startup.src
/quantum/qmset.src
..............................................................................
3.1.6 Testcase Validation
A full set of output for all tests is placed in test/Testoutput
for comparison and validation purposes. It is intended to be used
with test.com as follows:
test.com gnu G20 Testoutput 20
for the c20test tests to be run, where G20 is the test output
directory. The result is compared with the output in Testoutput,
and the pared-down diffs placed in G20.rpt.
A validation awk script is also submitted, comare.awk, which is
to be used to determine pass/failure and to report the relevant diffs
only.
awk -f compare.awk G30.rpt
will process G20.rpt and report PASS of FAIL based on relevant diffs
only. A more verbose output with the relevant diffs reported is
produced with:
awk -f compare.awk verbose=1 G20.rpt
Some tests were modified to get rid of extraneous stuff.
Files Added:
test/compare.awk
Files Modified:
test/c20test/noetest.inp
test/c23test/nose1.inp, nose2.inp
test/c24test/pbound1.inp
test/c26test/pathint.inp, tpnoe.inp
test/c27test/testeef1.inp, testeef1imag.inp
test/c30test/cq1ab1gbdyn.inp, cq1fsvvacu.inp, cq1fsvwat.inp
/cqmeohvacu.inp, cqnmawat.inp, cqtip4pbulk.inp
..............................................................................
3.1.7 Bugfixes
Fixes to code for compaq alpha mostly centered on emap code.
Some fixes are submitted here and at least the code compiles now, but
emap still broken.
(1) Added a note that GBMV requires GENBORN prefx name for compilation.
(2) Fixed FASTEW known incompatibility for CHEQ.
(3) Fixed timing bug in dynamics
(4) arg list missing vars in epath.src
(5) Fixed problem with integer*4 and integer*1 declarations in GBMV
(6) Bugfix of problem printing dihe constraints.
(7) GBSW source code moved from misc/ to energy/
(8) adumb/svdcmp.src modernization of do loops to accomodate f90 compiler
(9) SHELL code logical variable fix in anacor.src, correl.src, shell.src
(10) Timing bug in dynamics fixed.
(11) energy.src: Changes to fix redundant call to lonepair force remapping.
(12) gbmv.src: Removed integer*4/*1 declarations for correct performance
on ia64 and xlf machines. Modified to improve readability and
computational performance.
(13) gbsw timers and constants fixed.
(14) mcener.src and movead.src: PATHINT temporary fixes
(15) mcmini.src: BROKEN protection from steepd/neb disfunctional code
(16) abner.src: NEB problem moved inside if block
(17) nbexcl.src: fix for lrvdw when it is not specified in the nbond parameters
File moved:
source/energy/gbsw.src from source/misc
Files Modified:
build/UNX/Makefile_alpha, energy.mk, misc.mk
source/adumb/svdcmp.src
correl/anacor.src, correl.src, shell.src
dynamc/dcntrl.src, dynamc.src
emap/emapio.c, emapsubs.src,
energy/energy.src, epath.src, gbmv.src, gbsw.src
fcm/new_time.fcm, shell.fcm
io/parmio.src
machdep/cstuff.c, socket.c
mbond/mbback.src
mc/mcener.src, mcmini.src, movead.src, mvcrot.src, mvhmc.src, mvrtrn.src
minmiz/abner.src, steepd.src
nbonds/ewald.src, nbexcl.src, nbutil.src
util/new_timer.src
Modified Documentation:
doc/gbmv.doc, cheq.doc
------------------------------------------------------------------------------
3.2 Developments at the National Institute of Health
Name : Bernard R. Brooks
Email Address : brbrooks@helix.nih.gov
Institution : Laboratory of Biophysical Chemistry, NHLBI, NIH
Date : December 31, 2003
3.2.1 Holonomic constraints
The modification intends creation of a central point for all
holonomic constraints to ensure compatibility and consistency.
This provides a template for adding additive constraints.
File Added:
source/manip/holonom.src
Files Modified:
source/dynamc/dynamc.src, dynamc4.src, dynamcv.src, dynamln.src
/dynamvv.src, dynamvv2.src, mts.src, prssre.src, tps.src
/energy/energy.src, eutil.src
/manip/corman.src, shake.src
/minmiz/egrad1.src
/vibran/vibio.src, vibsub.src, vibutil.src
..............................................................................
3.2.2 CODES Extension
Extension to CODES to allow it to be called with a subset of
atoms. This allows non-CHARMM force fields to use varrious commands,
e.g., IC PARAM, that require a parameter lookup for particular atoms.
Files Modified:
source/correl/correl.src
/gener/genpsf.src, update.src
/manip/intcor.src, intcor2.src, shake.src
/misc/hbuild.src
/pert/pert.src
/quantum/qmset.src
..............................................................................
3.2.3 Callable Parser
Main program split. Main parser is now a callable routine and
allows a CHARMM command to invoke another command.
File Modified:
source/charmm/charmm_main.src
..............................................................................
3.2.4 VECTOR Codes Removed
Old FAST codes (PARVECT, CRAYVEC, CRAY, VECTOR) are removed. The
FASTer command allows three stage options, OFF, ON and DEFAult. The
default is to use fast scalar routines where available.
Files Removed:
source/energy/cenerf.src, enefst2.src, enefst2q.src, enefvect.src, enefvp.src
/fcm/cray.fcm
/image/cnbndm.src, imnbf2p.src, imnbfp.src
/mmff/enbfast_mm.src
/manip/cshake.src
/nbonds/cenbf.src, cnbnd.src, enbf2.src, evdwf.src, ewaldf2.src
/nbonds/nbndf2p.src, nbndfp.src
Files Modified:
source/cff/enbfast_cff.src
/charmm/iniall.src, miscom.src
/energy/anal.src, ecntrl.src, enefscal.src, epath.src
/fcm/dimens.fcm, fast.fcm
/fcm/
/mc/mcener.src, mcimge.src
/mc/
/mmff/efast_mm.src
/nbonds/enbfast.src, enbond.src, ewaldf.src, nbonds.src
/pert/epert.src
..............................................................................
3.2.5 Bugfixes and Clean-up
General cleanup, improving ## control...
Files Modified:
source/dynamc/dcntrl.src, dynio.src, lonepair.src, tpcontrol.src, trnphi.src
/fcm/fstshk.fcm, param.fcm, timer.fcm, tmd.fcm
/io/coorio.src, parmio.src
/manip/rotlsq.src
/mc/mcio.src
/misc/quicka.src
/mmff/enbscalar_mm.src
/nbonds/ewald.src
------------------------------------------------------------------------------
3.3 Developments at NIC-Slovenia
Names : Milan Hodoscek
Email Address : milan@cmm.ki.si
Institution : National Institutes of Chemstry, Ljubljana, Slovenia
Date : July 7, 2003
3.3.1 Parallelization of TMD code
Parallelization of TMD method completed
Files Modified:
doc/parallel.doc
source/dynamc/tmd.src
/energy/rmsd.src, ecnstr.src
/manip/rotlsq.src
..............................................................................
3.3.2 New global variable MDSTEP
Introduction of global variable for number of steps in the dynamics.
Before this was only for GRAPE module, now it is global.
Files Modified:
source/fcm/contrl.fcm, grape.fcm
/dynamc/dynamc.src
/nbonds/grape.src
..............................................................................
3.3.3 Trajectory files for QM charges from dynamics calculations
Writing of QM charges from GAMESS in the trajectory format. Since
GAMESS calculates 3 types of charges they are put into the trajectory file
in the following order: X - Mulliken; Y - Lowdin; Z - ESP charges.
Files Modified:
source/fcm/gamess.fcm, reawri.fcm
/charmm/iniall.src
/dynamc/dcntrl.src, dynamc.src
/gukint/gukini.src
..............................................................................
3.3.4. Support for new version of GAMESS
Newest GAMESS version 3 JUL 2003 (R1) is supported in CHARMM and
some fixes for the QM/MM interface
Files Modified:
source/fcm/gamess.fcm
/gukint/gukini.src
source/gamint/gamess/gamess.src,gmsnbo.src,grd1.src,grd2a.src,
/guess.src,inputa.src,inputb.src,inputc.src,
/int1.src,iolib.src,mccas.src,prplib.src,
/prppop.src,rhfuhf.src,scflib.src,
/unport.src,zunix.c
------------------------------------------------------------------------------
3.4 Generalized Born-Surface Area Model with Implicit Membrane (GBSA/IM)
Name : Velin Spassov, Lisa Yan, Sandor Szalma, Piotr Cieplak,
Krzysztof Olszewski
Email Address : kato@accelrys.com
Institution : Accelrys
Date : 12/18/03
GBSA/IM permits calculations of solvation energy and forces in presence
of Implicit Membrane as it is described in Spassov,V.Z, Yan, L and
Szalma S. J. Phys. Chem. B, 106,8726-8738 (2002). The calculations are
based on the simultaneous use of two CHARMM modules: GBIM and ASPENRMB.
GBIM module includes the effect of Implicit Membrane (IM) in the
calculations of the electrostatic contribution to solvation energy in
the frames of Generalized Born approach (see gbim.doc). GBIM module is
extended version of GENBORN module of B. Dominy and C.L. Brooks,III
(genborn.doc) where the membrane is added to molecular model as a planar
dielectric slab having the same dielectric constant as inside the molecule.
In addition to standard Gborn parameters, GBIM has optional parameters to
control the intramolecular dielectric constant, membrane thickness as well as
the position and orientation of membrane relative to coordinate system.
ASPENRMB is modification of ASPENR (aspenr.doc) by including Implicit
Membrane (IM) in Surface Area (SA) calculations. In GBSA/IM approach
ASPENRMB is used to calculate the non-polar contribution to solvation energy.
ASPENERMB can be also as a separate program to calculate solvation energy and
forces based on the solvent accessible surface area of each atom using Atomic
Solvation Parameters (ASP), as proposed by Wesson and Eisenberg.
In addition to standard ASP parameters, ASPENRMB uses optional parameters
to control the thickness as well as the position and orientation of
membrane relative to coordinate system. ASPENRMB is activated by reading
a surf file, as described in doc/aspenrmb.doc.
keywords: GBIM ASPMEMB
Remark: GENBORN and ASPENER must be present in pref.dat as well.
Files Added:
source/energy/gbim.src
/fcm/gbim.fcm, surfmemb.fcm
/misc/aspenermb.src
Files Modified:
install.com
source/charmm/charmm_main.src, iniall.src
/energy/energy.src, intere.src
/io/mainio.src
New Documentation:
doc/gbim.doc, aspenrmb.doc
New Testcase:
test/c31test/gbsaim.inp
------------------------------------------------------------------------------
3.5 Screened Coulomb Potentials Implicit Solvent Model (SCPISM)
Names : Sergio A. Hassan and Ernest L. Mehler
Email Address : mago@helix.nih.gov
Institution : CMM/DCB/CIT, National Institutes of Health (NIH);
WMC, Cornell University;
Mount Sinai School of Medicine (NYU)
Date : December 19, 2003
The SCPISM is an implicit solvent model (ISM) for macromolecules.
Parameterization of the model was carried out only for proteins, and
for use with the all-atom PAR22 forcefield.
The current version incorporates only a continuum approach for electrostatics
and optionally a simple term that accounts for hydrophobic effects (see
documentation in scpism.doc for details). The model is based on screened
Coulomb potentials (SCP). The current implementation is the initial step in a
long-term project aimed at developing a general implicit solvent model
(ISM) for macromoleculs, i.e., a continuum approach to describe both
electrostatic and non-electrostatic effects, to be used in large-scale
molecular mechanics simulations.
The current implementation is suitable only for dynamics simulation,
energy evaluation and minimization of peptides and proteins (any
CHARMM options are supported)
Files Added:
doc/scpism.doc
source/fcm/scpism.fcm
/misc/scpism.src
test/c31test/scpismtest.inp
/data/scpism.inp
Files Modified:
source/charmm/charmm_main.src
/nbonds/enbond.src
------------------------------------------------------------------------------
3.6 The University of Maryland Developments
Name : Victor Anisimov and Alexander D. MacKerell, Jr.
Email Address : victor@outerbanks.umaryland.edu
Institution : The University of Maryland School of Pharmacy
Date : December 29, 2003
3.6.1 Drude Oscillator Code Fixes
With the Drude polarizable model situations arise where atoms have
more than 8 bonds. A switch has been added that increases IATMXB to
20 when Drude particles are present in the system versus the default
value 8.
Declaration of KDRUDE variable is moved from drude.src to the PSFR
common block from which it can be shared by other routines.
Files Modified:
source/fcm/psf.fcm
/gener/drude.src
/nbonds/nbexcl.src
..............................................................................
3.6.2 Gaussian Input Generation
Gaussian input generation was changed to be compliant with Gaussian98
and Gaussian03 requirements. The three last rows of comments in the
input file created by CHARMM were removed since modern Gaussian
misinterprets them as ONIOM instructions.
The old Gaussian input generator allows printing coordinates of those
atoms only which have Z-matrix records. Other atoms will be omitted
thereby limiting the utility of the created file. The new generator
writes mixed Cartesian-internal coordinate file where all atoms
present in the system will be printed. This mode is activated by IC
GAUSS ZMIX keyword.
The mixed coordinate format is particularily useful for partial QM
geometry optimization of two rigid interacting molecules, e.g. a model
compound and a water molecule. Such cases are common in CHARMM
parameter optimization procedures where CHARMM optimized interaction
energies and geometries of two interacting molecules should be
verified against QM results. The first molecule is defined in the Gaussian
input file by Cartesian coordinates and second one is represented by
internal coordinates in an orientation relative to the first molecule.
Files Modified:
source/manip/wrgaus.src, intcor.src
doc/intcor.doc
..............................................................................
3.6.3 Fixed Origin for DIPOLE Calculation
Standard dipole calculation by CHARMM moves the dipole origin of ions
into geometric center of molecule. This becomes problematic when comparing
the CHARMM dipole moment with Gaussian QM data, since Gaussian does not
move the dipole origin. The OXYZ keyword is added to prevent the origin
move in CHARMM. The format of the command is COOR DIPOle OXYZ.
Files Modified:
source/correl/anacor.src, solana.src
/manip/corman.src
doc/corman.doc
..............................................................................
3.6.2 CMAP bugfix
With all trans phi, psi geometry CMAP energies are wrong. This is
due to a machine precision problems. offset values to avoid precision
problem.
File fixed:
soruce/energy/ecmap.src
------------------------------------------------------------------------------
3.7 Karolinska Institute Fixes and Enhancements
Name : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska Institute
Date : January 3, 2004
1. Added possibility to specify a "MODEL" to be read/written using
READ/WRITe COOR PDB.
Files modified:
io/coorio.src
doc/io.doc
2. Modified CORRel timeseries INERtia to allow user to extract the three
main moments of inertia of selected atoms.
Files modified:
correl/correl.src
doc/correl.doc
3. Added conversion of cartesian vector timeseries to spherical coordinates
in CORRel MANTime.
Files modified:
correl/mantim.src
doc/correl.doc
4. Modification to allow CORRel EDIT to modify VECCOD of individual
timeseries (previous
was to change VECCOD for all components of a vector timeseries)
Files modified:
correl/correl.src
5. Several modifications to NMR-module. Allow compact output of relaxation
parameters to file; write files that can be used as input for ModelFree
program; estimate entropy and effective correlation times of eg backbone NH
vectors; allow CSA contribution to relaxation rates; allow user to turn off
analytic calculation of overall rotation diffusion.
Files modified:
source/misc/nmr.src
doc/nmr.doc
6. Bugfix in calculation of solvent-site radial distribution function.
Files modified:
correl/solana.src
7. Bugfix in output of integration timestep from GTICNT.
Files modified:
dynamc/dynio.src
------------------------------------------------------------------------------
3.8 Harvard Developments
Name : Robert Petrella
Email Address : petrella@tammy.harvard.edu
Institution : Harvard University
Date : January 3, 2004
(1) Clustering for BYCC set up to be done by default just after
the exclusions are first made (after first call to UPDATE).
The NO_BYCC preprocessor "if" statements in the cluster-related
algorithms were removed in order to make this a default process.
Hence, the MKCLusters command is no longer necessary to use BYCC.
These changes also allow "active atom" selections for non-bonded
interactions to be coded easily into routines anywhere in charmm.
Files modified:
source/nbonds/nbutil.src, nbexcl.src, nbonds.src, nbndcc.src
/charmm/iniall.src
/fcm/actclus.fcm, exclar.fcm
(2) ATOMON array in eef1 was replaced by a global active atom array,
ACAFLG, which is either 1 or 0 depending on whether the atom is
active or not. This fixes a bug involving CONS FIX, eef1, and isolated
atoms.
Files modified:
source/misc/eef1.src
/energy/energy.src, intere.src
/mc/mcener.src
(3) Compiler optimization macros in build/UNX/nbonds.mk
were changed from FC0 to FC2 in the following cases: enbondg.f,
nbndcc.f, nbndgc.f and nbondg.f. This increases the speed of both
the default (BYGR) and BYCC list-generation routines, without
introducing any obvious compilation issues.
(4) Minor additional modifications to nbutil.src for printing out
correct non-bonded options.
File modified:
source/nbonds/nbutil.src
5) BYCC now handles atom clusters that are larger than the non-bonded
cutoff distance.
source/nbonds/nbndcc.src
------------------------------------------------------------------------------
3.9 University of Wisconsin Developments
Name : Qiang Cui and Guohui Li
Email Address : cui@chem.wisc.edu, gli@chem.wisc.edu
Institution : University of Wisconsin, Madison
Date : December 23, 2003
3.9.1 Block Normal Mode method and Gaussian (Anisotropic) Network Model
The BNM approach projects the full atomic hessian into a subspace
spanned by the eigenvectors of blocks, which reduces the size of the
eigenvalue problem dramatically. Each block can be defined by the user
in very flexible manners as an amino acid or a secondary structural
element. Currently only the T/R vectors of the blocks are included as
basis vectors.
The main code is vibblock.src, which constructs the projected hessian
in a direct manner, which is essential for applications to large systems
(e.g., ribosome). Vibblock.src requires input from vibran.src, and it
(through SUBROUTINE BLOCKHESSIAN) calls the subroutines that handle 2nd
derivative calculations. In the current version, only BOND, ANGLE,
UREY-BOND, DIHE, ImproperDIHE, Electrostatic, VDW and EEF1 terms are
supported. Three new variables (QBSECD,HSBLC,MAXD)
have been added to the list of arguments of these subroutines.
All source files (see the modified files list) that call these
energy subroutines have been changed; i.e., ".false.,0,0" was appended.
Both serial and parallel versions are supported. The parallel version
has only been tested on linux clusters with the "gnu M mpich" options.
For the diagonalization of large sparse matrices, the BNM code uses
the (P)ARPACK package, which can be downloaded for free from the PARPACK
website.
The Gaussian (Anisotropic) Network Model(GANM) has also been
implemented, and only the serial version is available now. The
calculation needs two files made by the user.
Files Added:
source/vibran/vibblock.src
/fcm/vibblock.fcm
Files Modified:
doc/vibran.doc
source/correl/anacor.src
/energy/energy.src, eintern.src, intere.src, ediff.src
/ecntrl.src, ecnstr.src
/image/eimage.src
/mbond/mbdiag.src
/mc/mcener.src
/misc/genetic.src, hbuild.src, eef1.src
/nbonds/nbonds.src, nbondg.src, nbonda.src, enbondg.src,
/enbonda.src, enbond.src
/pert/icfcnf.src, epert.src, icpert.src, tsme.src
/quantum/qmene.src
/vibran/vibran.src
New Testcases:
test/c31test/bnmtest.inp, ganmtest.inp
..............................................................................
3.9.2 SCC-DFTB/MM Free Energy Calculation
A Dual-Topology-Single-Coordinate (DTSC) approach has been implemented
for SCC-DFTB/MM free energy perturbation calculations. With DTSC,
which is very similar to PERT, free energy perturbations can be
carried out with SCC-DFTB/MM for chemical species with very similar
chemical strctures but different electronic distributions (e.g., redox
processes). With minor modifications, the code can now be used to
evaluate pKa's.
It MUST be used with "FAST OFF" in the CHARMM script because only
generic atom-atom codes have been modified so far.
Periodic boundary condition and cutoff for SCC-DFTB/MM electrostatics
have also been put in to facilitate solution studies; only
"Force-based" or "Energy-based" SHIFTs have been implemented.
Files Added:
source/fcm/blockscc.fcm
Files Modified:
doc/sccdftb.doc
source/energy/energy.src, eintern.src
/dynamc/dynio.src, dcntrl.src, dynamc.src, dynamc4.src
/dynamcv.src, dynamvv.src
/fcm/sccdftb.fcm, gamess.fcm
/gener/update.src
/image/upimag.src
/io/coorio.src
/mbond/mbback.src
/mc/mcio.src
/nbonds/enbonda.src, heurist.src
/pert/block.src
/sccdftbint/sccdftbini.src
/sccdftbsrc/dylcao.f, eglcao.f, externalchgrad.f,
/externalshift.f, gettab.f, mulliken.f, shift.f
[Note: testcases will be submitted by June 30, 2004.]
------------------------------------------------------------------------------
3.10 Force Field Developments
Name : Alex MacKerell
Email Address : alex@outerbanks.umaryland.edu
Institution : Univ. of Maryland School of Pharmacy
Date : January 19, 2004
3.10.1 Restructurinf RTF/PARAM Files
In version 31 a major restructuring of the topology and parameter
files was undertaken. This was performed to create a more modular
approach to the files, thereby avoiding the problem of files becoming
increasingly large. The restructuring was done such that the primary
topology and parameter files for biomolecules can be used as they were
previously. However, the topology and parameter information for the
majority of model compounds used in the parameter development,
additional molecules, including coenzymes, and patches parametrized to
be compatible with the CHARMM force fields have been moved to toppar
stream files. These toppar stream files have to be streamed in a
CHARMM input script typically following reading of the parent topology
and parameter files. They include both the topology and parameter
information for the selected molecules, using the "read rtf card
append" and "read param card append" commands to append the additional
information to the topology and parameter lists. As of version c31 it
is still necessary to maintain all the MASS atom lists in the parent
topology and parameter files.
Modified Documentation:
doc/energy.doc, io.doc, parmfile.doc, rtop.doc
..............................................................................
3.10.2 CMAP Parameter Addition
These are identical to the charmm22 force field except for the
addition of CMAP. Work is in progress on additional corrections to
the charmm22 force field that will be released as all31 or a later
version.
New protein topology and parameter files added:
toppar/top_all22_prot_cmap.inp, par_all22_prot_cmap.inp
..............................................................................
3.10.3 Non-CHARMM Parameters
topology and parameter files for BMS, AMBER and OPLS force fields.
See 00readme in the toppar/non_charmm subdirectory.
toppar/non_charmm/par_amber_98.inp, par_amber_cornell.inp
/par_bms_dec03.inp, par_opls_aa.inp
/par_opls_ligand.inp, top_amber_cornell.inp
/top_bms_dec03.inp, top_opls_aa.inp
The following are introduced and modified during the development period
of February 15, 2004 through August 15, 2004. The developments are
based on CHARMM c31a2. As declared at the CHARMM Meeting (Harvard
University, July 9-10, 2004), the following features are still under
development and not included in the c31 release versions:
Grand Canonical Monte Carlo (GCMC) GCMC
Block Normal Mode method VIBBLOCK
Gaussian (Anisotropic) Network Model VIBBLOCK
SCC-DFTB/MM Free Energy Calculation SCCDFTB
The SPASIBA Force Field SPASIBA
Endian Testing TESTENDIAN
------------------------------------------------------------------------------
4.1 TSRI Developments
Developers : Scott Brozell, Mike Crowley, Charles L. Brooks, III
Roberto GOmpers (SGI)
Email Address : sbrozell@scripps.edu, crowley@sripps.edu,
brooks@scripps.edu
Institution : The Scripps Research Institute
Date : July 4, 2004
4.1.1 4-Byte Integer Binary IO
64 bit integers are default for many architectures now.
Trajectories and other binary files written by charmm are unreadable
on other machines when the binary files contain 64 bit integers.
This mod makes all binary io restricted to 32 bit integers only
Files Modified:
install.com
source/correl/solana.src
/dimb/dimbsub.src
/dynamc/dynio.src
/dynsub.src
/fcm/iochan.fcm
/deflts.fcm
/gener/hbonds.src
/image/xtlfrq.src
/io/coorio.src
/parmio.src
/psfres.src
/machdep/cstuff.c
/machio.src
/manip/corman2.src
/intcor.src
/molvib/molvio.src
/nbonds/etable.src
/util/datstr.src
/title.src
/util.src
/vibran/rbquas.src
/redbas.src
vibio.src
Modified Testcase:
c31test/endian.inp
..............................................................................
4.1.2 Performance Enhancement of ENBFS8
Loop rearrangement and temporary arrays for locality to speed up
fast nonbond routine.
Files Added:
source/fcm/enbfs8p.fcm
source/nbonds/enbfs8p.src
Files Modified:
install.com
source/nbonds/enbfast.src
/util/new_timer.src
..............................................................................
4.1.3 64 bit Parallel and Serial IBMAIX Codes
Files Added:
build/UNX/Makefile_ibmaix
/Makefile_ibmaix64
/Makefile_ibmaixmp64
Files Modified:
install.com
source/correl/solana.src
/machdep/cstuff.c
/paral1.src
/paral2.src
/space.src
/manip/shake.src
/nbonds/pmeutil.src
------------------------------------------------------------------------------
4.2 Developments at the National Institute of Health
Developers : H. Lee Woodcock and Bernard R. Brooks
Email Address : hlwood@nih.gov, brb@nih.gov
Institution : Laboratory of Biophysical Chemistry, NHLBI, NIH
Date : July 1, 2004
4.2.1 Autogenerate for Patching Option
An autogenerate feature has been added to the RTF reader and the
PATCh command which allow the autogeneration of angles and dihedrals.
The PATCH command syntax:
PATCh misc-patch-spec residue-list-spec
misc-patch-spec ::= [SORT] [SETUp] [WARN] [ ANGLe ] [ DIHEdrals ]
[ NOANgle ] [ NODIhedral]
The RTF reader AUTOgenerate command syntax:
AUTOgenerate [ ANGLes ] [ DIHEdrals ] [ PATChes ] [ NONE ]
[NOANgles] [NODIhedrals] [NOPAtches]
Note that autogenerate is not the default and must be requested.
The specifications in the PATCH command override the specification
in the RTF.
Files Modified:
source/charmm/iniall.src
source/fcm/rtf.fcm
source/gener/genpsf.src
source/gener/modpsf.src
source/io/rtfio.src
..............................................................................
4.2.2 New MANTIM STATe and HEAViside Functions
CORRECL has two new operations, STATe and HEAViside.
MANTIME name { STATe minv maxv } ! Q(t) = 1 (minv < Q(t) < maxv), else = 0
{ HEAViside } ! Q(t) = 0 (when Q(t)<0), else = 1
Files Modified:
source/correl/correl.src
source/correl/mantim.src
..............................................................................
4.2.3 New Crystal type "RECTangular"
A new crystal type "RECTangle" has been added to the CRYStal DEFIne
command. This new type is the same as "ORTHorhombic", except that the
ratios of the unit cell dimensions are fixed. The total volume may change.
RECTangular - a/A = b/B = c/C and alpha = beta = gamma = 90.0 degrees.
(Note: A,B,C are the initial a,b,c values)
(example: 50.0 40.0 30.0 90.0 90.0 90.0 )
(volume = c*b*a)
(degrees of freedom = 1)
The undocumented ISOTropic option in the DYNAmics command has been removed,
since it never worked properly and the new code make its intended
function obsolete.
Files Modified:
source/dynamc/dynamvv2.src
source/dynamc/prssre.src
source/energy/energy.src
source/fcm/image.fcm
source/image/crystal.src
source/image/eimage.src
source/image/xtlfrq.src
source/mc/mcener.src
source/mc/mcmini.src
source/minmiz/abner.src
source/minmiz/conjug.src
source/minmiz/egrad1.src
source/minmiz/nraph.src
source/minmiz/powell.src
source/minmiz/steepd.src
source/minmiz/tndriv.src
source/misc/testch.src
source/pert/epert.src
..............................................................................
4.2.4 Add SCALAR WRITE Command
There is a new SCALar WRITe command to output data arrays in CHARMM.
File Modified:
source/manip/scalar.src
..............................................................................
4.2.5 New Expanded Fast Routines and Fast Control
A new set of FAST routines have been developed. These have been
written as a single routine that becomes expanded into many
"cleaned" routines that are free of unnecessary code (e.g. IF tests).
Use of these routines will significantly improve performance.
FAST OFF ! Use the slow full-feature routines
FAST GENEric ! Use the old "fast" routines (that are no longer fast)
FAST ON ! Use best routine available for current calculation
FAST EXPAnd ! Use new expanded routines
Files Added:
source/nbonds/enbaexp.src
source/nbonds/enbgexp.src
Files Modified:
source/charmm/miscom.src
source/energy/enefscal.src
source/energy/energy.src
source/energy/intere.src
source/fcm/fast.fcm
source/image/eimage.src
source/mbond/mbdiag.src
source/mc/mcimge.src
source/misc/genetic.src
source/nbonds/enbond.src
source/pert/epert.src
source/pert/icfcnf.src
source/pert/icpert.src
source/pert/tsme.src
source/vibran/vibblock.src
..............................................................................
4.2.6 Inline ERFC Code for Faster Ewald
The ERFC lookup table code has been simplified (fewer operations)
and now works with a zero distance (good for DRUDE), which eliminated
a pair of inner loop IF tests.
Files Modified:
source/cff/ewald_cff.src
source/fcm/ewald.fcm
source/mmff/enbscalar_mm.src
source/nbonds/ewald.src
source/nbonds/nbutil.src
..............................................................................
4.2.7 Improve the PRESsure INSTantaneous Command.
The PRESsure INSTantaneous command now works with a zero temperature.
Additional virial and pressure data is printed.
Files Modified:
source/dynamc/prssre.src
..............................................................................
4.2.8 NUMLP
Set ?NUMLP variable for the number of lonepairs.
Files Modified:
source/dynamc/lonepair.src
source/gener/psfsum.src
..............................................................................
4.2.9 PRNLEV Control
Change PRNLEV values to improve print control.
Files Modified:
source/energy/printe.src
source/image/images.src
source/nbonds/heurist.src
source/nbonds/nbonds.src
..............................................................................
4.2.10 Energy Call Control
To facilitate routine selection in ENBOND, a universal flag, QGCMC,
has been added. (Aaron, would you check on this? mctest02.inp seems to
generate energy blow-out. I fixed part of it, yet does not work correct.)
Files Modified:
source/charmm/iniall.src
source/fcm/gcmc.fcm
..............................................................................
4.2.11 Move ACE Code
The ACE common block code was added to a structured data file in
fcm/inbnd.fcm (which violates the rules governing structured data
files). It also inhibited further development of inbnd.fcm.
The ACE arrays have been moved to the file fcm/ace.fcm.
File Added:
source/fcm/ace.fcm
Files Modified:
source/charmm/iniall.src
source/dynamc/dcntrl.src
source/fcm/inbnd.fcm
source/io/mainio.src
source/manip/cstran.src
source/manip/scalar.src
source/mc/mc.src
source/mc/mcace.src
source/mc/mcener.src
source/nbonds/ace.src
source/nbonds/nbonds.src
source/nbonds/nbutil.src
source/util/selcta.src
..............................................................................
4.2.12 Set KBT and expand format statement
The variable KBT was not properly set.
File Modified:
source/dynamc/dcntrl.src
..............................................................................
4.2.13 Optional Exit for SHAKE Error
Added an optional exit for SHAKE tolerance exceeded errors.
By setting BOMLEV to 1 or more, you can make CHARMM die on this error.
File Modified:
source/manip/shake.src
..............................................................................
4.2.14 Fix bugs/problems with ##IF usage
There were a number of ##IF control problems. The use of the inline
precompile selection: !##IF CHEQ
is wrong. The correct syntax is !##CHEQ
Also, spaces within ## line identifiers is not allowed.
Files Modified:
source/fcm/param.fcm
source/fcm/traj.fcm
source/fcm/vibblock.fcm
source/image/upimag.src
source/vibran/vibran.src
..............................................................................
4.2.15 Fix QECONT and ATOMON Bugs
The use of QECONT and filling the ECONT array was wrong.
File Modified:
source/misc/eef1.src
..............................................................................
4.2.16 Fix SCALAR READ Parallel Bug
There was a bug in the SCALar READ command when used in a parallel
calculation. This has been fixed.
File Modified:
source/manip/scalar.src
..............................................................................
4.2.17 Fix Compile and Timer Bugs in SPAS Code
The SPAS code would not compile properly. It still does not work
and it consumes massive quantities of memory... The code should
be reworked or removed.
Files Modified:
source/energy/energy.src
source/io/parmio.src
..............................................................................
4.2.18 NUMBERs and CONSTANTs
The use of real*8 numbers in calling sequences has been corrected.
This is non-standard and causes problems on some compilers.
Also, I made an effort to make the use of constants more consistent.
For example, I replaced instances of 332.0... with the parameter CCELEC
in fcm/consta.fcm.
Files Modified:
source/dynamc/dynamcv.src
source/dynamc/dynamln.src
source/dynamc/dynamvv.src
source/dynamc/dynamvv2.src
source/energy/ecmap.src
source/energy/gbmv.src
source/energy/gbsw.src
source/fcm/consta.fcm
source/io/coorio.src
source/io/rtfio.src
source/mbond/mbback.src
source/mc/mcio.src
source/misc/genetic2.src
source/nbonds/pmeutil.src
source/util/random.src
..............................................................................
4.2.19 Fix Spelling
File Modified:
source/fcm/rndnum.fcm
..............................................................................
4.2.20 QM/MM Interface Using the Q-Chem Quantum Chemistry Package
Added a QM/MM interface to Q-Chem using the GAMESS-US and GAMESS-UK
interface as a model. Q-Chem and CHARMM communicate via files rather than
common blocks which means the two programs live separately.
The Q-Chem QM/MM interface was also extended to function with the
highly parallel Replica/Path and the Nudged Elastic Band Methods.
Files Modified:
install.com
source/charmm/charmm_main.src
source/charmm/iniall.src
source/energy/energy.src
source/fcm/gamess.fcm
source/fcm/replica.fcm
source/fcm/path.fcm
source/gener/update.src
source/gukint/gukini.src
source/nbonds/nbonda.src
source/nbonds/nbonds.src
source/quantum/addlnat.src
..............................................................................
4.2.21 Q-Chem Input Generation
Added the ability of zmat.src to write out Q-Chem input files. This
occurs in the same way that the Gausssian interface is used.
File Modified:
source/misc/zmat.src
..............................................................................
4.2.22 Off-Path Optimization and Simulation
The new EPATHO procedure was added which allows a user to run
orthogonal simulations at each replica/bead/point along a replica or
NEB path. These simulations are used to compute the free energy of
reaction.
Curvature corrections to these simulations were also added, but have
not been throughly tested to determine their usefulness.
Files Modified:
source/energy/epath.src
source/fcm/path.fcm
source/fcm/replica.fcm
source/fcm/gamess.fcm
------------------------------------------------------------------------------
4.3 Developments at NIC-Slovenia
Names : Milan Hodoscek
Email Address : milan@cmm.ki.si
Institution : National Institutes of Chemistry, Ljubljana, Slovenia
Date : June 30, 2004
4.3.1 New version of GAMESS supported
New version of GAMESS (19 May 2004 (R3)) is interfaced with
CHARMM. New features include Fragment MO, NMR shifts, improved
DFT convergence and many others.
Files Modified:
doc/gamess.doc
source/fcm/gamess.fcm
source/flucq/fluqqmmm.src
source/gamint/blur.src
source/gamint/ddi.src
source/gukint/gukini.src
source/gamint/gamess/{grd2a.src,int1.src,mccas.src,prplib.src,
prppop.src,prpel.src,unport.src,zunix.c,
gamess.src,grd1.src,guess.src,inputb.src,
inputc.src,iolib.src,scflib.src,rhfuhf.src,
inputa.src}
..............................................................................
4.3.2 Parallelization of DRUDE, LONEPAIR and VV2 integrator
DRUDE and VV2 integrator are parallelized. For efficiency also
LONEPAIR had to be parallelized.
Files Modified:
source/gener/drude.src
source/manip/holonom.src
source/machdep/paral1.src
source/energy/ediff.src
source/energy/energy.src
source/dynamc/lonepair.src
source/dynamc/dcntrl.src
source/dynamc/dynamvv2.src
source/dynamc/dynamcv.src
source/dynamc/dynamc.src
source/dynamc/dynio.src
source/nbonds/nbonds.src
..............................................................................
4.3.3 Parallelization of SSBP and GSBP
Spherical Solvent Boundary Potential method was parallelized.
General Solvent Boundary Potential method parallelization started.
Currently works in parallel environment, but not parallelized yet.
Files Modified:
doc/parallel.doc
source/energy/energy.src
source/misc/ssbp.src
source/misc/gsbp.src
source/misc/pbeq2.src
..............................................................................
4.3.4 Enhancements for GRAPE interface
Several enhancement in the GRAPE interface.
Files Modified:
source/nbonds/grape.src
..............................................................................
4.3.5 Fix and extension of SOLANA
The calculation of rotational correlation in SOLANA was wrong.
It is fixed and extended to use Legendre polynomials of second order,
by introducing new command keyword RLP .
Files Modified:
doc/corman.doc
source/charmm/iniall.src
source/correl/solana.src
source/fcm/corman.fcm
..............................................................................
4.3.6 Parallelization of RANDOM code and fix for NEWRNG
Parallelization of standard RANDOM number generator. Also the
usage of CLCG generator was fixed at the same time.
Files Modified:
source/charmm/iniall.src
source/correl/solana.src
source/dynamc/dcntrl.src
source/dynamc/dynamc.src
source/energy/gbmv.src
source/fcm/clcg.fcm
source/fcm/parallel.fcm
source/manip/intcor.src
source/mc/mc.src
source/misc/genetic.src
source/misc/pbeq.src
source/util/clcg.src
source/util/random.src
source/vibran/vibran.src
..............................................................................
4.3.7 Fixes for various ## keywords
Some of the ## keywords would not allow compilation of CHARMM if
excluded from pref.dat. New set of fixes for this are in:
Files Modified:
source/energy/eintern.src
source/energy/energy.src
source/nbonds/enbfast.src
source/nbonds/nbonds.src
source/mc/mcener.src
------------------------------------------------------------------------------
4.4 Harvard Developments
Name : Robert Petrella
Email Address : petrella@tammy.harvard.edu
Institution : Harvard University
Date : June 29, 2004
4.4.1 BYCC Enhancements
1) SUBROUTINE NBNDCC made into two routines:
NBNDCCF --for fastest execution, stripped of options
NBNDCCO --for compatibility with various options.
The latter routine is the one where developers should add functionality
to BYCC.
2) BYCC made compatible with heuristic updates
(for both atom-based and group-based calculations)
3) Changes in logic for calling cluster-generating routine
(SUBROUTINE CLSBYRULE).
A) Clusters are made by default prior to updating
the list if "BYCC" is specified in the update command
(unless they have previously been made).
B) An informed guess is made as to whether the connectivity
or the topology of the system has changed before calling
NBNDCC. If a change is detected, the clusters are
remade prior to non-bonded list generation. This is
done because changes in the connectivity may necessitate
the formation of new clusters, and significant changes in the
topology almost certainly do.
(changed subroutine: GTNBCT)
4) added global bycc QLBYCC in actclus.fcm to indicate BYCC
has been specified in non-bonded command (for use in other
parts of charmm).
5) minor modifications in eef1 code for compatibility with BYCC
6) BYCC made compatible with TSM
7) clustering algorithm made faster (now clusters
roughly 1,000,000 atoms/s on 2.66 GHz Pentium 4)
Files Modified:
source/charmm/iniall.src
source/nbonds/nbndcc.src
source/nbonds/nbonds.src
source/nbonds/nbutil.src
source/misc/eef1.src
source/fcm/actclus.fcm
------------------------------------------------------------------------------
4.5 Developments at University of Vienna
Developers : Tibor Rudas, Stefan Boresch and Othmar Steinhauser
Email Address : tibi@mdy.univie.ac.at and stefan@mdy.univie.ac.at
Institution : Molecular Dynamics and Biomolecular Simulation group
at the Department of Theoretical Chemistry and
Molecular Structural Biology, University of Vienna
Date : June 23, 2004
4.5.1 COM Centering in COOR DIPO
When calculating the dipole moment of a set of atoms carrying a total
net charge the coordinates of this set are recentered to the center of
geometry of these atoms. Adding a MASS keyword to the invocation (which
is present for many other COOR commands) allows the center of mass as
locus of recentering.
Both this keyword and the recently introduced OXYZ keyword (which
avoids this recentering unsing the absolute coordinates) are also
introduced into the DIPO series of CORREL.
All calls to CDIPOLE are updated but where no use/parsing of a MASS
keyword is provided/necessary .FALSE. and 0 are passed instead of MASS
and AMASS (solana.src)
Files Modified:
source/correl/correl.src
source/correl/anacor.src
source/correl/solana.src
source/manip/corman.src
Modified Documentation:
doc/corman.doc
doc/correl.doc
..............................................................................
4.5.2 SHELLs of Different Thickness
Instead of the (still supported) keyword SHTH which defines a single
thickness used for all shells generated shells of different thickness
can be defined by using the new SHBO keyword.
Following this keyword should be NSHL real numbers which represent the
boundaries between the single shells (so these numbers should all be in
increasing order).
Files Modified:
source/fcm/shell.fcm
source/correl/shell.src
source/charmm/iniall.src
Modified Documentation:
doc/shell.doc
Modified Testcase:
test/c31testshell.inp
------------------------------------------------------------------------------
4.6 Karolinska Institute Fixes and Enhancements
Developer : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska Institute
Date : July 1, 2004
1) Added possibility to compute water-dipole rotational correlation fcn (P1
or P2), also works in shell defined by RSPIN & RSPOUT
Files Modified:
source/correl/solana.src
doc/corman.doc
test/c27test/solanal2.doc (seemed unnecessary to add another file for this)
2) Set CHARMM variable CFNORM to the normalization used in CORREL CORFUN,
and added possibility to supply the normalization value to be used by
CORFUN; useful to get correctly normalized partial correlation fcns.
Files Modified:
source/correl/solana.src
source/correl/correl.src
source/correl/corfun.src
doc/correl.doc
doc/subst.doc
3) Added substitution variables CPUTIME and ELATIME
Files Modified:
source/machdep/machutil.src
doc/subst.doc
4) Corrected documentation of defaults for CORREL CORR (Legendre pol. P0 is
a constant..)
File Modified:
doc/correl.doc
------------------------------------------------------------------------------
4.7 Implicit Membrane Model 1 (IMM1) and EEF1 update
Developer : Themis Lazaridis
Email Address : tlazaridis@ccny.cuny.edu
Institution : City College of New York/CUNY
Date : May 17, 2004
IMM1 is an extension of the EEF1 implicit solvation model to lipid
membranes. The membrane hydrocarbon interior is modeled as cyclohexane,
with a smooth, monotonic transition between the interior and the aqueous
region.
Electrostatic screening is modeled using a modified distance-dependent
dielectric function (eps=r**l, where l depends on the position of the
two atoms with respect to the membrane.
In addition, updated parameters for EEF1 are provided (referred
to as EEF1.1) and also a version of EEF1 based on CHARMM22.
Files Added:
support/aspara/toph19_eef1.1.inp
support/aspara/param19_eef1.1.inp
support/aspara/top_all22_prot_eef1.inp
support/aspara/top_all22_prot_eef1.1.inp
support/aspara/solvpar22.inp
Files Modified:
source/fcm/eef1.fcm
source/energy/energy.src
source/energy/intere.src
source/misc/eef1.src
source/nbonds/enbfast.src
support/aspara/solvpar.inp
Modified Documentation:
doc/eef1.doc
------------------------------------------------------------------------------
4.8 Multiple Gaussian Job Input Generation
Developers : Victor Anisimov and Alex D. MacKerell, Jr.
Email Address : victor@outerbanks.umaryland.edu
Institution : University of Maryland
Date : June 28, 2004
Gaussian program uses "--link1--" string to separate multiple jobs.
On the other hand hyphen symbol is treated by CHARMM as line continuation
instruction. As a result, CHARMM was merging the "--link1--" string,
which is a Gaussian instruction, with the next line. A correction has
been made to instruct the CHARMM command line reader to turn off the line
continuation mechanism for the moment of Gaussian file generation.
The command line parser ignores hyphen symbol when the parser is
invoked from G94INP routine. Logical variable USEHYP is introduced
for this purpose. USEHYP set to .TRUE. enables line continuation
mechanism (CHARMM default). USEHYP set to .FALSE. disables line
continuation (call from G94INP routine).
File Modified:
source/util/parse.src
------------------------------------------------------------------------------
4.9 SASA Changes and Enhancements
Developers : Urs Haberthuer and Amedeo Caflisch
Email Address : atlantis@bioc.unizh.ch, caflisch@bioc.unizh.ch
Institution : University of Zurich, Switzerland
Date : July 3, 2004
The keywords to modify the SASA parameters from within the CHARMM input
file were changed for clearer usability. This concerns the keywords to
modify the radii, probabilistic parameters, and connectivity parameters
for the surface calculations. The keywords to modify the surface-tension
like solvation parameters were also changed. See the SASA documentation
for the new syntax.
Two keywords, INFX and SURF, were added. INFX causes the fixed exclusion
atoms to be considered for the surface calculations. (By default, they
are neglected for historical reasons. See the SASA documentation for
more detailed explanations.) SURF causes the approximated atomic solvent
accessible surface areas to be stored in WMAIN.
Lazaridis and coworkers introduced the CHARMM atom type CR in
param19_eef1.inp and toph19_eef1.inp. This atom type is now considered
explicitly in the SASA code although all the SASA parameters for CR are
identical to those for the CHARMM atom type C.
Some code cleanup and adjustments of the documentation within the SASA
code were performed.
Files Modified:
doc/sasa.doc
source/fcm/sasa.fcm
source/misc/sasini.src
source/misc/sasene.src
The following are introduced and modified during the development period
of August 15, 2004 through February 15, 2005. The developments are
based on CHARMM c31b1.
5.1 TSRI Developments
Developers : Mike Crowley and Charles L. Brooks, III
Email Address : crowley@sripps.edu, brooks@scripps.edu
Institution : The Scripps Research Institute
Date : December 30, 2004
5.1.1 AFM Reset
The reset command is added to afm. This permits the afm commend to
be run in a loop with all data structures cleared in between.
Files modified:
doc/afm.doc
source/energy/afm.src
source/fcm/afm.fcm
..............................................................................
5.1.2 Clean-Up
Some code cleanup and prefx labeling to make debugging easier.
Files modified:
source/energy/energy.src
source/energy/eutil.src
source/nbonds/enbfast.src
source/util/prpref.src
..............................................................................
5.1.3 GBMV Bugfix
We fixed a number of issues related to the performance and correctness of
the GBMV code on serial and parallel machines.
Files modified:
source/energy/gbmv.src
source/fcm/gbmv.fcm
..............................................................................
5.1.4 Huge Version
HUGE keysord added to code and install.com for million atom systems.
Files modified:
install.com
source/fcm/dimens.fcm
source/fcm/heap.fcm
source/fcm/stack.fcm
..............................................................................
5.1.5 Makefile Update
Updated osx and gnu Makefiles
Files modified:
build/UNX/Makefile_osx
build/UNX/Makefile_gnu
..............................................................................
5.1.6 Testcase Fixes
Small fixes to test cases to correct poor design of some test cases and
to add some functionality to others.
Files modified:
test/c31test/nebdiala.inp
test/c31test/afm.inp
test/c31test/nebdialapmf.inp
test/c31test/off_path_simulation.inp
..............................................................................
5.1.7 Timing Fixes
Timer debugging added to prevent double timing and other timing errors.
Files modified:
source/fcm/new_time.fcm
source/util/new_timer.src
..............................................................................
5.1.8 NEWRNG Code Removed
NEWRNG produced bad results, code removed to recover old results.
Files modified:
source/charmm/iniall.src
source/correl/solana.src
source/dynamc/dcntrl.src
source/dynamc/dynamc.src
source/dynamc/dynio.src
source/energy/gbmv.src
source/fcm/exfunc.fcm
source/manip/intcor.src
source/mc/mc.src
source/misc/genetic.src
source/misc/pbeq.src
source/util/random.src
source/vibran/vibran.src
------------------------------------------------------------------------------
5.2 Developments at the National Institute of Health
Developers : H. Lee Woodcock, Xiongwu Wu and Bernard R. Brooks
Email Address : hlwood@nih.gov, wuxw@nhlbi.nih.gov and brb@nih.gov
Institution : Laboratory of Biophysical Chemistry, NHLBI, NIH
Date : December 30, 2004
5.2.1 SGLD Bugfix
The local average velocities are accumulated twice in the SGLDW
subroutine.
File Modified:
source/dynamc/sglds.src
------------------------------------------------------------------------------
5.3 SASA Enhancements and Bugfixes
Developers : Urs Haberthuer, Riccardo Pellarin, and Amedeo Caflisch
Email Address : atlantis@bioc.unizh.ch, pellarin@bioc.unizh.ch,
caflisch@bioc.unizh.ch
Institution : University of Zurich, Switzerland
Date : December 30, 2004
(1) New Surface Parameters
A new keyword, NEWP, is added. It triggers the use of a new set of
values for the radii, probabilistic parameters, and connectivity
parameters. (These parameters are used to calculate atomic solvent
accessible surface areas within the SASA module.) The new set was
derived in 2002 by Haberthuer and it gives a better correlation with
exact analytical surfaces than the original Hasel and Still surface
parameters.
(2) Images
Image lists are now supported in SASA. This allows to use SASA for
simulations with periodic boundary conditions.
(3) Documentation
The SASA documentation itself and also the documentation within the
SASA code is updated.
(4) Miscellaneous
The atom type C1ES is now supported by SASA and the format of the output
of the SASA module slightly changed.
(5) Bugfixes
The SASA module did not work correctly for simulations with constant
pressure since the call to the subroutine SASENE in the subroutine
ENERGY was at the wrong place. This has been corrected.
An empty nonbond exclusion pair list could crash the SASA module. This
bug is now fixed.
Files Modified:
doc/sasa.doc
source/energy/energy.src
source/fcm/sasa.fcm
source/misc/sasini.src
source/misc/sasene.src
------------------------------------------------------------------------------
5.4 Karolinska Institute Fixes and Enhancements
Developer : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska Institute
Date : December 30, 2004
(1) SINGLE precision version cannot be created due to use of non-generic
forms of intrinsic functions in several routines. I updated prefx.src with
these, and also had to make some changes to source files.
CHARMM created with SINGLE in pref.dat is however NOT fully functional.
Timing routines (elapsed time) do not work, parallel jobs hang (I only tried
socket communication), charges do not sum up correctly at psf generation;
there may be other problems as well. It would be useful to have this
working correctly again.
Files modified:
tool/prefx.src
source/adumb/eadumb.src
source/emap/emapdock.src
source/util/selcta.src
(2) Set values of BOMLEV, IOLEV, PRNLEV variables at startup, corrected
a typo in FTCPWRT call
Files modified:
source/charmm/charmm_main.src
(3) Allow echeck to be turned off by specifying a negative value; not
documented.
Files modified:
source/dynamc/dynamc.src
(4) Some format changes to allow for large step numbers to print correctly.
Files modified:
source/dynamc/dynsub.src
(5) Format change to allow larger heap allocations to be correctly reported.
Files modified:
source/machdep/space.src
