ChangeLog.c27
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CHARMM 27 |
| c27a1 |
Developmental |
September 30, 1998 |
| c27a2 |
Developmental |
February 15, 1999 |
| c27b1 |
Release |
August 15, 1999 |
| c27b2 |
Release |
February 15, 2000 |
| c27b3 |
Release |
August 15, 2000 |
| c27b4 |
Release |
February 15, 2001 |
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About CHARMM27 Development |
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As an on-going project, CHARMM development will be carried out with
CHARMM version 27 series. We set up the base revision c27 out of
c26a2. The following describes new features and enhancements
incorporated during the c27 development period.
The following are introduced and modified during the development period
of February 15, 1998 through September 15, 1998.
1.1 Monte Carlo Simulation Module
Name : Aaron R. Dinner
Email Address : dinner@tammy.harvard.edu
Institution : Harvard University
Date : June 1, 1998
The module provides commands to allow the construction of a move set
for an arbitrary molecule (represented by a standard CHARMM PSF) and
the use of that move set in canonical and multicanonical Monte Carlo
simulations. Speed and flexibility are gained by separating the
bookkeeping associated with a move (the MOVE subcommands) from the actual
application of that move to the molecule (the MC command).
The primary MOVE subcommand is MOVE ADD, which determines all the
locations that a move type can be applied to a subset of atoms (each
location is a move instance) and, for each instance, the relevant rotation
axes and centers, the moving atoms, and the relevant bonded terms. Thus,
each call of MOVE ADD results in a group of move instances with the same
move type. The available pre-defined move types are rigid translations
of residues (RTRN), rigid rotations of residues (RROT), single atom
displacements (CART), simple torsion rotations (TORS), and concerted
rotation of 7 (or, in the case of an end, 6) torsions (CROT). Each of
these can be applied to an arbitrary subset of atoms using standard CHARMM
SELE...END statements. In addition, MOVE ADD associates with each group
of move instances a set of parameters (set by the optional arguments)
associated with manual and automatic optimizations of the move set.
Additional MOVE subcommands are provided to edit move parameters, delete
move groups, and read and write move groups.
The MC command performs the loop over the appropriate number of dynamics
steps. Each step consists of: randomly picking a group of move instances
(weighted), randomly picking an instance from that group (unweighted),
calculating the energetic contribution of the moving atoms and their images,
applying the move, calculating the new energetic contribution, applying
the acceptance criterion, updating automatic move size optimization counters
if necessary, and finally performing any desired I/O (at present, only
trajectory writing is enabled).
Files Added:
source/mc/armupt.src
/mc/mc.src
/mc/mcener.src
/mc/mcimge.src
/mc/mcio.src
/mc/mcuser.src
/mc/movead.src
/mc/moveio.src
/mc/mvcrot.src
/mc/mvdihe.src
/mc/mvrtrn.src
/mc/numrec.src
source/fcm/mc.fcm
Files Modified:
source/charmm/iniall.src mc.fcm added to the INCLUDE statements.
NMVTYP initialized to zero.
ISDMC initialized to an arbitrary value.
LCENTR initialized to .TRUE.
BIMAGC freed with FREEDT.
source/charmm/charmm_main.src Added MOVE and MC to command IF-ELSE structure
source/nbonds/enbfast.src These three files were modified to allow
/nbonds/enbond.src suppression of the calculation of the group
/nbonds/enbondg.src centers during each call of the energy routine
(in MC, they are carried on the heap, rather
than on the stack, and updated only when they
are changed).
source/energy/energy.src These twelve files were modified due to a change
/energy/intere.src in the calling sequence of ENBOND to allow
/image/eimage.src restriction of the range of INBLO elements
/mbond/mbdiag.src checked in ENBFS8, ENBFV8, and EVDW.
/misc/genetic.src
/nbonds/enbfast.src Note that EVDWF was NOT changed. In this case,
/nbonds/enbond.src the time to do one step scales as O(N), so a
/nbonds/enbonda.src complete scan over the system goes as O(N^2).
/pert/epert.src
/pert/icfcnf.src
/pert/icpert.src
/pert/tsme.src
/energy/energy.src These three files were modified due to a change
/image/eimage.src in the calling sequence of EIMNBD to allow
/pert/epert.src restriction of the range of IMBLO elements
checked in ENBFS8, ENBFV8, and EVDW (via ENBOND).
New Documentation:
doc/mc.doc
New Testcase:
test/c26test/mctest01.inp
/c26test/mctest02.inp
test/data/rgds_wat30.psf
/data/rgds_wat30.crd
/data/bpti_allh.crd
------------------------------------------------------------------------------
1.2 Implicit Solvation Model (EEF1)
Name : Themis Lazaridis
Email Address : themis@tammy.harvard.edu
Institution : Harvard
Date : June 22, 1998
Implicit solvation model to be used in combination with PARAM 19.
I used some of the ASP features for this. I enclose all the code in
"IF ASPENER" loops and I use the ASP energy term for reporting my
solvation free energy.
Files Added:
source/misc/eef1.src
/fcm/eef1.fcm
support/aspara/toph19_eef1.inp
/aspara/param19_eef1.inp
/aspara/solvpar.inp
Files Modified:
source/charmm/charmm_main.src to parse the command EEF1
/energy/energy.src to call eef1 energy
New Documentation:
doc/eef1.doc
New Testcase:
test/c26test/testeef1.inp
/data/testeef1.crd
/data/toph19_eef1.inp
/data/param19_eef1.inp
------------------------------------------------------------------------------
1.3 Updates and Modifications for Multi-Body Dynamics
Name : Robert Nagle, Masa Watanabe, Donovan Chin, and
Ryszard Czerminski
Email Address : rnagle@moldyn.com
Institution : Moldyn Inc
Date : June 30, 1998
1.3.1 MAJOR ENHANCEMENTS to MBO(N)D interface
1) MOLDYN Code Distribution
MOLDYN code is available in academic versions as of c27a1. New soruce
module source/moldyn is added. Note the following links in the source/fcm
directory:
ln -s ../moldyn/HANDS2.INC .
ln -s ../moldyn/HEAPMB.INC .
ln -s ../moldyn/IFIRST.INC .
ln -s ../moldyn/INTGRL.INC .
ln -s ../moldyn/PARAM.FOR .
ln -s ../moldyn/SPECIF.INC .
2) Constant velocity (atomistic and multi-body)
A constant velocity method has been developed for use with DYNA (right
now, only works with LEAP and LOBATTO--MBO(N)D--integrators). The main
purpose of this facility was to run simulations similar to atomic force
microscopy. The constant velocity method, therefore, is used in
conjunction with the NOE facility to apply a 'spring' between the moving
atom and an atom on the target. This facility was used to study ligand
extractions from proteins (Dont forget to 'pin' protein about its center
of mass), and to compare movements of myosin with AFM experiments.
Note that the constant velocity pull is also available directly through
CHARMM, without having to go through MBO(N)D.
3) Langevin dynamics for bodies and particles
A prototype method for Langevin multi-body dynamics has been
implemented. Friction coefficients may be specified for EVERY
avaialble degree of freedom (3 for particles, 6+nModes for each body).
4) Single parameter method for mode generation
Generating reasonable body-based modes is a crucial part of MBO(N)D.
These modes are used for modeling flexible bodies. In recent years, there
have been several research papers in which people described a simple approach
to generate reasonable thermal fluctuations of proteins. In the approach,
a single parameter harmonic potential was used instead of the more complicated
force field. Based on their observations, low-frequency mode-vectors
generated by this simple potential are in good agreement with those calculated
from the full potential.
From the MBO(N)D point of view, this approach for generating body-based
modes is attractive. The instantaneous structure can be treated as an
equilibrium structure in this approach so that no artificial energy
minimization is necessary. Other approaches, i.e. using the full CHARMM
poteintail, require small steps of energy minimization before generating
modes because inappropriate modes may be produced from slight distorted
peptide-plains. In the same vein, no negative frequency eigenvectors are
generated with harmonic modes. In the regular MBO(N)D mode generation
approach, several of the body-based modes are usually of negative-frequency.
However, harmonic potential approach will eliminate these problems altogether.
References:
1. M.M. Tirion, Phys. Rev. Letts., 77, 1905 (1996)
2. I. Bahar, A. R. Atilgan, and B. Erman, Folding & Design, 2, 173 (1997)
..............................................................................
1.3.2 MINOR Enhancements
1) New keyword THRESHOLD in multi-body dynamics
This controls detection of Euler singularities and is generally
intended for developer use only.
2) Modification for initial body fitting
An improved flexible body fitting algorithm (used in DYNA STARt or
DYNA RESTart).
3) Improved error messages
4) Changes for better memory usage within the multibody code.
5) multibody code now compiles with -n32 and -64 SGI compiler flags
6) header reports MBOND size (memory) limits
..............................................................................
1.3.3 Bugfixes
1) Fixed problem with resetting of hinge on/off on repeated invocations
of multibody.
2) Intrabody energies (& forces) for flexible bodies were not being
computed correctly
Files Added:
source/dynamc/cveloci.src
/fcm/cveloci.fcm
/fcm/mbspp.fcm
Files Modified:
source/charmm/charmm_main.src
/charmm/iniall.src
/dynamc/dcntrl.src
/dynamc/dynamc.src
/energy/energy.src
/energy/eutil.src
/fcm/mbmts.fcm
/fcm/mbond.fcm
/fcm/mbpar.fcm
/mbond/mbback.src
/mbond/mbdiag.src
/mbond/mbdyn.src
/mbond/mbmodes.src
/mbond/mbmts.src
/mbond/mbond.src
/mbond/mbsub.src
/mbond/modtrans.src
/nbonds/nbonda.src
/nbonds/nbondg.src
/nbonds/nbonds.src
New/Modified Documentation:
doc/mbond.doc
doc/dynamic.doc
New Testcases:
test/c26test/mbtest28.inp
/c26test/mbtest29.inp
/c26test/mbtest30.inp
/data/mod_toph19_dumm.inp
/data/mod_param19_dumm.inp
/data/cor_dumm.psf
/data/cor_dumm.crd
------------------------------------------------------------------------------
1.4 Langevin-Normal Mode Multiple Time Step Algorithm
Name : Tamar Schlick, Adrian Sandu, Eric Barth
Email Address : schlick@nyu.edu
Institution : New York University
Date : June 30, 1998
This is an implementation of the LN algorithm (so called for its origin
in a Langevin/Normal-mode scheme) which applies an efficient force-splitting
(or multiple timestep) procedure to a stochastic formulation for dynamic
simulations. Detailed descriptions of the algorithm and background can be
found in the following works:
1. E. Barth and T. Schlick, "Overcoming stability limitations in biomolecular
dynamics. I: Combining force splitting via extrapolation with Langevin
dynamics in LN", J. Chem. Phys., August 1998 issue (in press).
2. E. Barth and T. Schlick, "Extrapolation versus impulse in multiple-
timestepping schemes. II: Linear analysis and application to Newtonian
and Langevin dynamics", J. Chem. Phys., August 1998 issue (in press).
3. A.Sandu and T.Schlick, "Further analysis of impulse and extrapolation force
splitting approaches in molecular dynamics", in preparation, 1998.
4. T. Schlick, E. Barth, and M. Mandziuk, "Biomolecular dynamics at long
timesteps: Bridging the timescale gap between simulation and
experimentation", Annu. Rev. Biophys. Biomol. Struc. 26: 179--220, 1997.
The algorithm relies on existing CHARMM force splitting routines under
the MTS command. The LN slow forces are incorporated via extrapolation as
opposed to "impulses" as in the MTS-RESPA method. This alleviates severe
resonance problems and permits larger outer timesteps to be used for
additional speedup.
The LN algorithm is compatible with SHAKE and with the use of boundary
conditions. Any other combinations of options have not been tested.
There are several parameters that are set for a LN simulation:
1. Langevin parameter gamma (FBETA in CHARMM notation), the damping constant:
* Recommended value = 5 to 20 ps^(-1)
Too small a value will render the simulation unstable. On the other
hand, the larger gamma is, the greater the overdamping of the
low-frequency modes. The above recommendation reflects a balance
found by experimentation. Gamma can also be simulation-goal dependent.
2. Timestep Protocol for force splitting:
Dt(fast) = inner TIMESTEP for updating the "fast" forces
* Recommended value = 0.5 -- 1 fs (no shake)
1 -- 2 fs (with shake)
Dt(medium) = K1*Dt(fast), update frequency for "medium" forces
* Recommended value = 1 -- 3 fs
Dt(long) = K2*Dt(medium), update frequency for "slow" forces
* Recommended value = 6 -- 200 fs
Larger computational savings can be realized with a larger Dt(long).
However, the speedup is limited and reaches an asymptotic value
since the evaluation of medium forces becomes increasingly costly.
The asymptotic maximum speedup can be reached for outer timesteps of
24 or 48 fs, for example, but the precise value depends on the timestep
protocol employed and the application system. This should be tested
carefully by the user for the problem at hand.
3. Definition of the force splitting classes:
Recommended Protocol --:
* Fast forces = BOND 1, ANGL 1, DIHE 1
* Medium forces = Nonbond cutoff
cutoff distance = 6 A - 8 A
healing region = 1 A - 3 A
buffer region = 1 A - 3 A
SLFG RSCUT [cutoff distance] RHEA [healing region] BUFF [buffer region]
* Longrange forces = remaining terms
The nonbonded pairlist is updated in the current implementation
every Dt(long).
4. The GROUP electrostatics option works much better than ATOM electrostatics.
Use of the latter is discouraged based on our test problems.
PLEASE NOTE: All the LN parameters above can be sensitive to the
----------- specific protocol used for the dynamics simulations
and are problem dependent (see discussion of results
in the LN papers).
For further guidance, feel free to contact Tamar
Schlick at the email: schlick@nyu.edu
Files Added:
source/dynamc/dynamln.src
Files Modified:
source/dynamc/dcntrl.src
source/fcm/tbmts.fcm
Modified Documentation:
doc/mts.doc
New Testcase:
test/c26test/lnx_img.inp
test/data/solvbpti.crd
------------------------------------------------------------------------------
1.5 PBEQ Enhancements
Name : Benoit Roux and Wonpil Im
Email Address : imwo@plgcn.umontreal.ca
rouxb@plgcn.umontreal.ca
Institution : University of Montreal, Department of Chemistry
Date : 14/07/1997
PBEQ module in CHARMM now supports a variety of utilities;
the IO manipulation, the calculation of non-cubic cells, focussing,
simple geometrical objects (sphere, cylinder), the optimization of the
over-relaxation parameter, the interpolation of boundary conditions,
and, the B-spline charge assignment.
The code is slighlty optimized and a variety of utilities are added.
One can READ the electrostatic potential written in binary format.
Facilities for non-cubic cells are added. Spherical and cylindrical
regions of uniform dielectric constant may be added to a system.
To save computational time for boundary conditions, zero boundary
conditions and the interpolation method can be used. And to get a more
precise boundary conditions, the focussing method can be used.
To speed up the iterative solution, the over-relaxation parameter
can be optimized. To remove discontinuities in the reaction field
forces, the 3rd-order B-splines charge interpolation over nearest 27
grid points can be used. The source code (pbeq.src) and the common
block (pbeq.fcm) can be ported to c26a3 since the module is almost
standalone (porting should be straightforward).
Files Modified:
source/misc/pbeq.src
source/fcm/pbeq.fcm
test/data/radius.str
Modified Documentation:
doc/pbeq.doc
New Testcase:
test/c26test/pbeqtest3.inp
Other Comments:
A typo for histidine in radius.str has been corrected in this version.
------------------------------------------------------------------------------
1.6 TSRI Developments and Bugfixes
Name : Charles L. Brooks, III and Mike Crowley
Email Address : brooks@scripps.edu, crowley@scripps.edu
Institution : The Scripps Research Institute
Date : July 30, 1998
1.6.1 Generalized Born Model (CLB: 5/6/98)
Files Added:
source/energy/genborn.src
source/fcm/genborn.fcm
Files Modified:
source/charmm/charmm_main.src
source/charmm/iniall.src
soruce/energy/energy.src
soruce/energy/eutil.src
soruce/energy/printe.src
soruce/manip/scalar.src
soruce/util/selcta.src
soruce/fcm/energy.fcm
New documentation:
doc/genborn.doc
New Testcases:
test/c26test/genborn1.inp
..............................................................................
1.6.2 Generalized(MultiCanonical) MD method. (CLB: 3/18/98)
Files Added:
source/misc/multicanon.src
source/fcm/mltcanon.fcm
Files Modified:
soruce/charmm/charmm_main.src
soruce/charmm/iniall.src,
soruce/energy/energy.src
..............................................................................
1.6.3 Soft van der Waals and Genetic Algorithm Code Fixed.
Introduced changes to correct problems with code for soft van der
Waals and genetic algoritm code. (CLB/MV: 3/18/98)
Files Modified:
source/gener/update.src
source/misc/genetic.src
source/misc/genetic2.src
source/nbonds/nbutil.src
source/fcm/inbnd.fcm
New Testcases:
test/c26test/tsoft.inp
test/c26test/softwater.inp
Modified documentation
doc/nbonds.doc
..............................................................................
1.6.4 SYSTem and Start-up
The SYSTem command is fixed and start-up coded is fixed so t3e can
read command-line options in CHARMM. (clbiii)
Files MOdified:
source/machdep/machutil.src
source/machdep/startup.src
Modified Documentation:
doc/miscom.doc
..............................................................................
1.6.5 NBFIX Problem on 2.0.2.21 unicosmk CRAY T3E, IRIX64 6.4
Routines parrdr and addnbf in source/io/parmio.src are optimized by
the compiler in a way that a counter, NBFIXN, is not globally updated even
though it is in common. Earlier bugfix, B980112.ep resolved the
problem for sgi compilers, but produced the same problem for t3e
compiler.
Added NBFIXN to the crgs of the calls to ADDNBF() and used the name
NBFIXNT in the dummy args of ADDNBF() and set NBFIXN=NBFIXNT inside ADDNBF().
Otherwise, the t3e compiler does not keep the value of NBFIXN in the common
block in param.fcm current. Errors in the vdw for runs with modified
parameters result otherwise.
File Modified:
source/io/parmio.src
..............................................................................
1.6.4 install.com (MFC)
Modified to allow for gmake on t3e and to support f90, keepf and POSIX.
..............................................................................
1.6.7 Bugfixs for C90/T90
correl/solana.src
dynamc/dynamvv.src
energy/ehbond.src
energy.src
fcm/mmff.fcm
number.fcm
io/parmio.src
machdep/machio.src
manip/cshake.src
mmff/enbfast_mm.src
nbonds/cenbf.src
cnbnd.src
enbf2.src
enbonda.src
evdwf.src
nbondg.src
nbonds.src
pert/epert.src
------------------------------------------------------------------------------
1.7 Karolinska Institutet Developments and Bugfixes
Name : Lennart Nilsson
Email Address : Lennart.Nilsson@csb.ki.se
Institution : Karolinska Institutet, Sweden
Date : June 26, 1998
1.7.1 COOR HBONd Overhaul
The command is overhauled to provide more descriptive output, and to
allow for analyses of contact not involving Hbonds (called as COOR CONTact).
Also the option COOR HISTogram is added to compute atom densities.
Files Modified:
source/manip/corman.src
/manip/corman3.src
/manip/hbanal.src
doc/corman.doc
New Testcase:
test/c26test/corhist.inp
..............................................................................
1.7.2 MERGe RECEnter
This is added to allow a trajctory run with PBC to be changed such that
a selected set of atoms (the solute) is in the center. Useful before analysis
of solute-solvent interactions.
Files Modified:
source/dynamc/dynsub.src
doc/dynamc.doc
New Testcase:
test/c26test/recenter.inp
..............................................................................
1.7.3 COOR ANALysis
More work done on the COOR ANALys module. Fixed minimum image correction
for MSD calculation, got the 3D histogramming to work.
Files Modified:
source/correl/solana.src
doc/corman.doc
New Testcases:
test/c26test/solvhist.inp
test/data/turnwat14.chr
..............................................................................
1.7.4 TRAJectory Command
Changed TRAJ command to accept the generally used trajectory syntax
(FIRSTU, NUNIT, ...)
File Modified:
source/dynamc/dynsub.src
..............................................................................
1.7.5 SOCKET Code
Added code to let CHARMM script remove slave processes after job-crash
(in SOCKET communication enviroments).
Files Modified:
source/machdep/paral1.src
/machdep/cstuff.c
..............................................................................
1.7.6 Bugfixes
(1) NDEGF was not correctly taken into account in TEMP timeseries in correl,
resulting in incorrect temperatures
FILES: source/correl/anacor.src
source/correl/correl.src
(2) Velocities not saved for all atoms in dynamic runs on parallel
systems. (veloctities were not distributed before being written)
FILES: source/dynamc/dcntrl.src
source/dynamc4.src
source/dynamcv.src
source/dynamcvv.src
(3) NSAVV not correctly reported after writing velocities (NSAVC was used).
FILES: source/dynamc/dynamc.src
source/dynamc/dynio.src
(4) Parallel timing output wrong for slave processes. Indexing problem.
FILE: source/machdep/paral1.src
(5) Declaration order problems cleared up in pmeutil.
FILE: source/nbonds/pmeutil.src
(6) DEC ALPHAMP - missing libraries when loading.
FIlE: install.com
(7) End-of-buffer error messages under DigitalPVM when empty buffers
encountered, added lenght checks in a couple of places.
FILE: source/machdep/paral1.src
------------------------------------------------------------------------------
1.8 Adaptive Umbrella Sampling Simulation
Name : Christian Bartels
Email Address : cb@brel.u-strasbg.fr
Institution : Institut le Bel, ULP Strasbourg
Date : August 11, 1998
Supports (multidimensional) adaptive umbrella sampling simulations.
The module provides commands to define degrees of freedom along which
adaptive umbrella potentials are applied during molecular dynamics
simulations. Statistics on the sampling of the degrees of freedom are recorded
during the md simulations and periodically used to update the umbrella
potentials such that uniform sampling of the degrees of freedom can be
expected. Currently, dihedral angles and the potential energy are supported
as degrees of freedom.
If several degrees of freedom are defined, multidimensional adaptive
umbrella sampling is performed.
Note that all changes are conditional and can be removed by deleting
the ADUMB flag in pref.dat.
References
1. C. Bartels & M. Karplus (1997) J. Comp. Chem. 18, 1450-
2. C. Bartels & M. Karplus (1998) J. Phys. Chem. B, 102, 865-
3. M. Schaefer, C. Bartels & M. Karplus (1998) J. Mol. Biol.
Files Added:
adumb/cmds.src process adaptive umbrella sampling commands
adumb/eadumb.src calculate umbrella coordinates and their derivatives
adumb/eval.src routines to analyze adaptive umbrella sampling runs
adumb/svdcmp.src singular value decomposition
adumb/umb.src update and apply adaptive umbrella potentials
fcm/umb.fcm definitions
Files Modified:
fcm/dimens.fcm dimensions of some arrays
fcm/exfunc.fcm definition of functions
charmm/charmm_main.src branch to adaptive umbrella sampling commands
charmm/iniall.src some initialization
energy/energy.src adaptive umbrella potential term; update statistics
energy/eutil.src new energy term ADUMB
energy/printe.src
fcm/energy.fcm
correl/correl.src WHIST (weighted histogram) command
correl/mantim.src
dynamc/dynamc.src writing of umbrella coordinate
dynamc/dynamc4.src
dynamc/dynamcv.src
dynamc/dynamvv.src
UNX/Makefile_* add adumb library
install.com add -f adumb.mk to make command
turn ADUMB switch on in pref.dat
New Documentation:
doc/adumb.doc
New Testcase:
adumb-phichi.inp 2D dihedral angle adaptive umbrella sampling
adumb-enum.inp potential energy adaptive ubrella sampling
ace2.inp peptide folding simulation
------------------------------------------------------------------------------
1.9 Analytical Continuum Solvent (ACS) Potential
Name : Michael Schaefer and Christian Bartels
Email Address : schaefer@brel.u-strasbg.fr
Institution : Institut le Bel, ULP Strasbourg
Date : 11 Aug. 1998
The analytical continuum solvent (ACS) potential is introduced to
perform molecular dynamics calculations with a continuum approximation
of the solvent.
Two solvent contributions to the effective (free) energy of a solute
are included: the electrostatic solvation free energy, and the
non-polar (i.e., non-electrostatic) solvation free energy.
The first (electrostatic) contribution (G_el) is calculated using an
analytical approximation to the solution of the Poisson-equation
called ACE (from: analytical continuum electrostatics).
The non-polar solvation free energy (G_np) is approximated by a pairwise
potential which yields results that are very similar to the well-known
surface area approximations of the hydrophobic (solvation) energy
(e.g., Wesson and Eisenberg, ASP potential in CHARMM).
All changes are conditional and can be removed by deleting the ACE
flag in pref.dat.
Reference for the electrostatic ACE potential:
M. Schaefer & M. Karplus (1996) J. Phys. Chem. 100, 1578-1599.
Reference for the ACS (G_el + G_np) potential:
M. Schafer, C. Bartels & M. Karplus (1998) J. Mol. Biol., in press.
Files Added:
nbonds/ace.src ACS energy
nbonds/acean.src ACS utility routines
Files Modified:
nbonds/enbond.src call to ACS energy
nbonds/nbutil.src parse ACE commands
charmm/charmm_main.src call ACE parser
charmm/iniall.src initialization of some variables
energy/printe.src print ACE energies
energy/eutil.src
io/parmio.src read effective volumes
manip/scalar.src enable manipulation of volumes and charge radii
fcm/energy.fcm some definitions
fcm/exfunc.fcm
fcm/inbnd.fcm
fcm/param.fcm
minmiz/tnpack.src need to include dimens.fcm (due to change in inbnd.fcm)
minmiz/nbutil.src
nbonds/ewaldf.src renamed ESELF to LESELF (due to name conflict)
nbonds/ewaldf2.src
nbonds/pme.src
install.com add ACE to pref.dat by default
New/Modified Documentation:
nbonds.doc reference to ace.doc added
ace.doc
New/Modified Parameters:
toppar/param19-1.2.inp effective volumes added tp param19 file
New/Modified Testcase:
c27test/ace1.inp minimization with ACE
c27test/ace2.inp peptide folding simulation
Data/toph19-1.2.inp
------------------------------------------------------------------------------
1.10 NIH Developments (I)
Name : Bernard R. Brooks
Email Address : brbrooks@helix.nih.gov
Institution : National Institutes of Health
Date : August 19, 1998
1.10.1 Paticle Mesh Ewald (PME) Upgrade
The PME code continues to be developed along several lines. This has
been a concerted effort. New features include:
FINIte option added (allows PME to be used on isolated systems)
more efficient (removal of 4 index arrays)
better parallelization
additional correction terms
net dipole term as an option
Files modified:
fcm/pms.fcm
nbonds/pme.src
nbonds/pmeutil.src
nbonds/nbutil.src
..............................................................................
1.10.2 Overhaul and Extention of IC Table Facility (INTCOR)
The IC facility in CHARMM has been extensively modified. All large
arrays have been moved to the HEAP and there are several new features.
We have developed most of these new features to assist in developing new
Monte-Carlo scripts. New features include:
several new commands and options, such as "IC GENErate"
IC GENErate - generate an IC table based on connectivity
new facility for efficient Monte-Carlo in IC space
SAVE and RESTORE commands have been modifed and extended (for MC)
IC tables moved to the HEAP
New parsing option, @@, to assist with MC docking, etc.
Files modified:
charmm/charmm_main.src
energy/ecnstr.src
fcm/bases.fcm
fcm/image.fcm
fcm/intcr.fcm
gener/genpsf.src
gener/modpsf.src
gener/replica.src
image/images.src
image/upimag.src
io/mainio.src
manip/intcor.src (major changes)
manip/intcor2.src (major changes)
misc/genetic.src
pert/puic.src
pert/tsms.src
quantum/addlnat.src
util/cmdpar.src
util/parse.src
vibran/redbas.src
vibran/vibio.src
vibran/vibran.src
vibran/vibsub.src
..............................................................................
1.10.3 Holonomic Constraints
Rigid body holonomic constrained dynamics (and minimizations) has been
developed. This yeilds the same trajectory as SHAKEing all atoms pairs,
but is much faster and more accurate. Also allows works for planar and
linear molecules (where SHAKE can't be used).
Other developments related to holonomic constraints include:
Problems with holonomic constraints fixed
Some minimization problems fixed
Fix up SHAKE with PERT
LONEpair PRINT command now lists all lonepair atoms
Allow DELETE ATOM command with lonepairs on.
QHOLO usage modified
Files modified:
dynamc/lonepair.src
fcm/pshake.fcm
gener/genpsf.src
manip/shake.src
minmiz/abner.src
minmiz/conjug.src
minmiz/egrad1.src
minmiz/powell.src
minmiz/steepd.src
minmiz/tndriv.src
pert/icfix.src
..............................................................................
1.10.4 SHAPES Facility
The resurrection of the SHAPES code has been completed (for now) with
several new features added;
general SHAPE restraints
shape manipulation
shape analysis
docking based on shape
Files modified:
charmm/iniall.src
dynamc/dcntrl.src
energy/energy.src
fcm/shapes.fcm (new)
gener/update.src
shapes/eshape.src
shapes/mdlio.src
shapes/shapedyn.src
shapes/shapes.src
..............................................................................
1.10.5 COOR SEARCH Command Overhauled
"COOR SEARch" has been extended for shapes and for more facile multiple
use (Allows docking based on SHAPE and charge distributions,...).
COOR SEARCH command now saves parsing and other data in a common block data.
COOR SEARCH Can add grid point "atoms" to the PSF
Files modified:
charmm/iniall.src
gener/genpsf.src
manip/corman.src
shapes/eshape.src
shapes/mdlio.src
shapes/shapedyn.src
shapes/shapes.src
..............................................................................
1.10.6 READ MDL with MMFF
The "READ MDL" command is extended to work with MMFF and "IC GENERate".
CHARMM can now automatically read a molecule from a MOL file, generate a PSF,
add hydrogens as needed, generate an IC table, build coordinates and minimize
This works in a loop, allowing throughput screening
Files modified:
mmff/mmff.src
manip/intcor2.src
..............................................................................
1.10.7 TEST FIRST in 4 Dimensions
The "TEST FIRSt" command is extended to the 4th dimension (##FOURD).
Files modified:
misc/testch.src
..............................................................................
1.10.8 SGMD Code
Shaomen Wang's Self Guided Molecular Dynamics (SGMD) code is added
to CHARMM. This is a partial implementation which is for testing purposes
only (includes parsing and the MD part).
Files modified:
charmm/iniall.src
dynamc/dcntrl.src
dynamc/dynamc.src
energy/energy.src
dynamc/meanf.src (new)
fcm/fbias.fcm (new)
..............................................................................
1.10.9 Constant Temperature Constraint Method
Files modified:
dynamc/dcntrl.src
dynamc/dynamc.src
fcm/reawri.fcm
..............................................................................
1.10.10 Substitution Parameters
Substitution parameters are set on "TRAJ READ" and a new "TRAJ QUERy"
command. READCV now set substitution parameters.
Files modified:
dynamc/dynio.src
io/trajio.src
..............................................................................
1.10.11 Move Major Data Structures to HEAP
There has been a concerted effort towards the reduction of CHARMM's
memory requirments Serveral data structures have been modified.
PERT, Internal Coordinates,
Files modified:
charmm/charmm_main.src (PERT)
fcm/bases.fcm (PERT)
fcm/epert.fcm (PERT)
fcm/mmff.fcm (MMFF unused data)
fcm/pert.fcm (PERT)
image/nbondm.src (PERT)
image/upimag.src (PERT)
manip/shake.src (PERT)
misc/genetic.src (GENETIC)
misc/genetic2.src (GENETIC)
mmff/assignpar.src (MMFF)
mmff/escalar_mm.src (MMFF)
mmff/readpar.src (MMFF)
nbonds/nbonda.src (PERT)
nbonds/nbondg.src (PERT)
nbonds/nbonds.src (PERT)
pert/epert.src (PERT)
pert/pert.src (PERT)
io/mainio.src (PERT) (ICDYN from KK)
dynamc/dynamc.src (ICDYN from KK)
dynamc/dynamcv.src (ICDYN from KK)
dynamc/dynamvv.src (ICDYN from KK)
energy/ecnstr.src (ICDYN from KK)
fcm/icpert.fcm (ICDYN from KK)
pert/icfcnf.src (ICDYN from KK)
pert/icpert.src (ICDYN from KK)
..............................................................................
1.10.12 Overhaul of vdW Table Usage
The vdw table has been partially overhauled. This is a first step.
What has been gained:
Reduction of memory
Fully functional "READ PARAm APPEnd"
No limit of vdw atom types (within reason)
Files modified:
energy/ediff.src
energy/energy.src
energy/intere.src
fcm/dimens.fcm
fcm/fast.fcm
gener/update.src
image/eimage.src
io/parmio.src
mbond/mbdiag.src
mmff/efast_mm.src
mmff/enbfast_mm.src
mmff/assignpar.src
nbonds/cenbf.src
nbonds/enbf2.src
nbonds/enbfast.src
nbonds/enbond.src
nbonds/evdwf.src
nbonds/ewald.src
nbonds/heurist.src
nbonds/nbexcl.src
nbonds/pme.src
nbonds/pmeutil.src
pert/block.src
pert/epert.src
pert/tsme.src
..............................................................................
1.10.13 Overhaul of SCALar Command
There are several new SCALar features and operations, such as the
direct access to stored arrays (e.g. "SCALar 9 SUM 8" )
Files modified:
manip/scalar.src
util/selcta.src
..............................................................................
1.10.14 FNDU and FNDROT Overhaul
When I was developing the rigid body dynamics, I found a much more
elegant and accurate way to perform these functions using simple anti-symmetric
tensor algrebra, so I discarded the old ones I wrote in back in 1983.
Files modified:
manip/rotlsq.src
..............................................................................
1.10.15 DYNA FORMAT and DYNA UNFORMAT
The file format of the card trajectory files has been modified.
This was necessary for very long simulations and to properly handle
constant pressure trajectories.
Files modified:
dynamc/dynio.src
..............................................................................
1.10.16 COOR Command Bugs
Fixed a bug in the XMOV, YMOV, and ZMOV substitution variables
(had wrong sign). Fixed a bug in the use of exclusions in the COOD DIST
command. Also modified the printout to give total counts and residue
types of selected atom distances.
Files modified:
manip/corman2.src
manip/corman3.src
..............................................................................
1.10.17 READ COOR FREE
READ COOR FREE is added. RAED COOR also reads weighting array data.
Files modified:
io/coorio.src
..............................................................................
1.10.18 CORREL Bugfix
Bug in correlation function by FFT for arrays longer than 32768.
There was an I*4 overflow condition for the normalization of correlation
functions when the FFT method was used.
Files modified:
correl/corfun.src
..............................................................................
1.10.19 NOE Assign
Exponent value printed in NOE ASSIGN command.
Files modified:
misc/noe.src
..............................................................................
1.10.20 Conditional Compile Modifications
Missing ##IF PBOUND is added.
Files modified:
charmm/miscom.src
..............................................................................
1.10.21 Problems with SQRT(ZERO)
SQRT(ZERO) doesn't always give ZERO. Some changes were made
to avoid this problem. These changes were not made throughout CHARMM.
Files modified:
correl/anacor.src
correl/corrio.src
correl/mantim.src
dynamc/dcntrl.src
dynamc/dynamc.src
..............................................................................
1.10.22 Preparing for Fortran90
Some files were modified to bring the code up to modern standards.
This includes;
DO loops end on different lines
DO loop ends are non-instructions (CONTINUE or ENDDO)
Get rid of Holerith data type
Remove PAUSE lines (replace by CALL WRNDIE)
Files modified:
correl/clustr.src
correl/cordyn.src
energy/enst2.src
graphics/graphx.src (removed OS2 junk)
image/xtlfrq.src
io/parmio.src
io/rtfio.src
misc/mmfp.src
misc/ssbp.src
misc/testch.src
molvib/gfdiag.src
molvib/gmat.src
molvib/molvio.src
molvib/molvsb.src
molvib/molvut.src
rxncor/path.src
solvation/coorman.src
solvation/deriv.src
solvation/rismio.src
solvation/soluu.src
solvation/soluv.src
solvation/solvation.src
solvation/solvv.src
solvation/state.src
util/imsl.src
util/matrix.src
..............................................................................
1.10.23 STRDT
Unused routine removed.
Files modified:
util/datstr.src
..............................................................................
1.10.24 Comments Added
Files modified:
fcm/psf.fcm
------------------------------------------------------------------------------
1.11 NIH Developments (II)
Name : Milan Hodoscek
Email Address : milan@kihp6.ki.si
Institution : National Institutes of Health
Date : August 19, 1998
1.11.1 Minimization Trajectory
Numerical first derivatives and trajectory creation option for ABNR
minimization method are added.
Files modified:
fcm/contrl.fcm
minmiz/egrad1.src
minmiz/minmiz.src
..............................................................................
1.11.2 Parallel Fixes
(1) Timestamp coding added to allow better profiling.
(2) "IF(IOLEV.LT.0) RETURN" was added to the MERGE command.
(3) New TEST NOCOmmunication command is added.
Files modified:
dynamc/dynamc.src
dynamc/dynsub.src
energy/energy.src
fcm/parallel.fcm
fcm/timer.fcm
image/upimag.src
machdep/cstuff.c
machdep/paral1.src
machdep/paral2.src
machdep/paral3.src
machdep/socket.c
machdep/xdisp.c
misc/testch.src
util/title.src
..............................................................................
1.11.3 Graphics Enhancements
Added an [NBAT integer] option to the graphics MAKE command (for the
LIGHT program).
Files modified:
graphics/drawit.src
..............................................................................
1.11.4 Blur - GAMESS development
GAMESS has been extended to allow external point changes to be
diffused by a 3-dimensional gaussian.
File added:
gamint/blur.src
Files modified:
gamint/gamini.src
machdep/cstuff.c
quantum/addlnat.src
..............................................................................
1.11.5 New GRAPE Code
Files added:
fcm/grape.fcm
nbonds/grape.src
Files modified:
charmm/iniall.src
nbonds/nbutil.src
util/sort.src
------------------------------------------------------------------------------
1.12 Consistant ForceField
Name : William S. Young
Email Address : wyoung@msi.com
Institution : MSI
Date : August 14, 1998
MSI has incorporated the Consistant ForceField (CFF) into CHARMM. CFF is a
class II forcefield that includes a set of eight cross in addition to bond
streching, angle bending, dihedral angles and out of plane deformation. The
CFF uses a 9-6-1 form for non-bond interactions.
Files Added (module/file.src):
cff/codes_cff.src
cff/efscalar_cff.src
cff/enbfast_cff.src
cff/enbonda_cff.src
cff/escalar_cff.src
cff/ewald_cff.src
cff/parrdr_cff.src
fcm/cff.fcm
Files Modified (module/file.src):
fcm/consta.fcm
fcm/dimens.fcm
fcm/energy.fcm
fcm/ffield.fcm
fcm/param.fcm
charmm/iniall.src
charmm/miscom.src
energy/ecntrl.src
energy/eutil.src
energy/intere.src
energy/printe.src
gener/genpsf.src
gener/update.src
io/parmio.src
io/psfres.src
manip/intcor2.src
nbonds/enbond.src
nbonds/nbexcl.src
New/Modified Documentation:
doc/cff.doc
------------------------------------------------------------------------------
1.13 Bugfixes
(1) B980623.rn
- Robert Nagle
Any HBONDS update can possibly produce a segmentation violation
(certainly an array bounds violation). In HBEDIT, no check made when
using IHB(I) - it may already have the value MARK (i.e. -999999).
File: source/gener/hbonds.src
(2) B980630.rs1
- Roland Stote
The EXTENDED Electrostatics model is not properly implemented.
In the Extended Electrostatics model, the electrostatic energy
is taken as the sum of a 'near' term plus an 'extended' term. The near
term is calculated as a standard pairwise sum and a group truncation
should be applied. The extended term is approximated by a multipole
expansion model and the van der Waals term is the standard pairwise
sum with a switching function.
In the recent versions of CHARMM, a switching function is applied
to the near term to which the extended term was added.
This leads to the exclusion of some electrostatic interactions
in the switching/truncation region.
Files: source/nbonds/enbfast.src (ENBFSG)
source/nbonds/enbond.src
(3) B980630.rs2
- Roland Stote
The default in the T3E version of c26a2 is to exclude the BLOCK routines.
This, in turn, excludes parts of the GROUP energies that should not
be excluded and different energies are obtained when compared
to other platforms.
File: source/nbonds/enbfast.src (ENBFSG)
(4) B980629.wy and B980728.wy
- William Young and Tom Halgren
There are a number of errors in the current implementation of MMFF in
CHARMM. When testing of the charmm version of MMFF, a large number of
differences were found in computed energies from the original OPTIMOL
version. These problems have been corrected. Also the atom typing
error was fixed.
Files: source/energy/ecntrl.src
source/mmff/assignpar.src
source/mmff/datastruc.src
source/mmff/escalar_mm.src
source/mmff/merckio.src
source/mmff/mmfftype.src
source/nbonds/enbond.src
source/fcm/mmff.fcm
(5) B980830.clb
- Charles L. Brooks, III and Michal F. Crowley
The variables xold, yold and zold are not initialized for atoms
outside the "parallel block" for parallel runs (using the routine
dynamc.src) with images and fixed atoms but are passed onto image
centering routines where they are used causing a floating point
exception on machines that don't force all uninitialized variables to
initialize to zero.
File: dynamc/dynamc.src
(6) B980902.br
- Simon Berneche (bernechs@magellan.umontreal.ca)
The gradient of energy is computed by using the position in the 4th
dimension instead of the forces.
File: minmiz/egrad1.src
The following are introduced and modified during the development period
of September 16, 1998 through February 15, 1999.
2.1 TSRI Developments and Bugfixes
Name : Charles L. Brooks, III and Mike Crowley
Email Address : brooks@scripps.edu, crowley@scripps.edu
Institution : The Scripps Research Institute
Date : January 8, 1999
2.1.1 Clean-Up
Uninitialized variables and/or poor programming practices are fixed.
Files modified:
source/adumb/eval.src, umb.src
/charmm/charmm_main.src
/correl/solana.src
/dynamc/dcntrl.src, dynamln.src
/fcm/cff.fcm, impnon.fcm, tbmts.fcm
/image/cnbndm.src, nbondm.src
/io/psfres.src, rtfio.src
/machdep/machio.src, machutil.src
/misc/multicanon.src
/nbonds/ace.src, nbexcl.src
/pert/icfcnf.src
/rxncor/path.src
2.1.2 Switching Function (SWITCH) for the Generalized Born Code
The CHARMM switching function for the generalized Born code is added.
The pref keword GBSWIT (to be specified in pref.dat) is also introduced for
the switching function.
File modified:
source/energy/genborn.src
2.1.3 Spatial List Builder - BYCUBE
A spatial (bycube) list builder compatible with images is added.
Both primary and image lists are produced simulataneously using the cube
method. This is useful mainly for long dynamics runs at constant volume.
Note:
(1) The new pref.dat keyword IMCUBES is required to activate the code.
(2) New CHARMM command keyword in any energy related command, i.e., nbond,
update, energy, dynam, mini is BYCBim.
(3) Currently not implemented for TSM, REPLICA, extended electrostatics,
anything that requires group lists.
Files added:
source/image/nbndgcm.src
test/c27test/bycbtest.inp (new testcase)
Files modified:
source/charmm/iniall.src
/fcm/deflts.fcm
/fcm/inbnd.fcm
/io/parmio.src
/nbonds/nbonds.src
/nbonds/nbutil.src
doc/nbonds.doc
build/UNX/image.mk
------------------------------------------------------------------------------
2.2 Cluster Cube Fast Nonbond List Generation Method
Name : Robert J. Petrella
Email Address : petrella@tammy.harvard.edu
Institution : Harvard University
Date : January 10, 1999
(1) BYCC: ATOM-BASED CALCULATIONS: (keyword "ATOM"):
The by-clusters-in-cubes, or BYCC, algorithm is a combination of the
BYCUbes algorithm, written by J. Thomas Ngo (June, 1990), and the BYGRoups
algorithm, written by Bernard R. Brooks (Aug 22, 1981). BYCC first places
the system in a cubical grid, as BYCU does, and then does distance
comparisons on clusters of atoms, as BYGR essentially does, rather than on
individual atoms. Both steps allow for a reduction in the number of atoms
passed to the final interatomic distance loop, speeding the calculation.
The use of both the cubical compartmentalization and atomic grouping
techniques in BYCC allows for greater efficiency than is possible using
either technique alone, and for this reason BYCC is generally faster than
either BYCU or BYGR. Also, because the routine does the final atom-atom
distance calculations, the exclusions, and the formation of the non-bonded
list all in one final loop, only a cluster-cluster pairwise list needs to be
stored internally to the routine as a work array. Thus, the memory
requirements are reduced relative to BYCU, which stores a much longer
atom-atom pairwise list (essentially a second non-bonded list) internally.
A requirement for the atom-based calculations is that clusters of
atoms need to be created (but see below for GROUP-BASED). A cluster is
a set of atoms that have mutually close connectivity relationships.
The topology of clusters is defined in the cluster file, which is read
into CHARMM by the user. The MKCLuster command then generates the actual
clusters of atoms by applying the information in the cluster file to the
structure (much like a .psf is generated from a topology file and an AA
sequence). The topology of the clusters is currently left to the
discretion of the user , although defaults are provided. The only
requirements in the formation of clusters are:
(a) the order of atoms as defined in the cluster file for each
residue must be the same as that in the RTF/PSF.
(b) clusters must be "continuous." That is, if a the high and low
atom numbers in a given cluster are 10 and 15, the atom numbers
11 through 14, if they exist, must be part of that cluster and
none other.
(c) the size of the largest cluster (i.e. the largest intracluster
atom-to-atom distance) cannot exceed the non-bonded cut-off distance.
(2) BYCC: GROUP-BASED CALCULATIONS (keyword "GROUP")
The main difference between the atom- and group-based implementations
of the BYCC algorithm is that the use of atomic clusters is omitted for
the group-based calculations. Extended electrostatics are fully supported.
New Commands:
READ CLUSter
MKCLuster
NBONd BYCC
Files Added:
source/fcm/actclus.fcm containing active and cluster info
/fcm/exclar.fcm contains exclusion arrays for atom and group-based
exclusions in a compressed table form.
/nbonds/nbndcc.src contains the nonbonded list generating routines:
SUBROUTINE NBNDCC for atom-based calculations
SUBROUTINE NBNDGG for group-based calculations
Files Modified:
build/UNX/nbonds.mk include nbndcc.src processing
doc/ ??? something should be done. may be nbonds.doc?
source/charmm/charmm_main.src
calls to two subroutines MKCLUST and NBACTV
/fcm/inbnd.fcm add logical variable LBYCC
/fcm/deflts.fcm add DFLBCC and DULBCC to logical variables
/io/parmio.src add IF(INDXA(COMLYN,COMLEN,'BYCC').GT.0) THEN
and modify BYGR and BYCU cases as appropriate
/io/mainio.src add call to RDCLUS
/io/rtfio.src add SUBROUTINE RDCLUS
/manip/corman3.src add SUBROUTINE SQUAREUP
/nbonds/nbonds.src add call to NBNDCC and separate HEAP allocation
section for NBNDCC
/nbonds/nbexcl.src add two subroutines relating to exclusion table:
SUEXTAB sets up mkextab, which generates
the exclusion table.
MKEXTAB
/nbonds/nbutil.src modified in several places (designated "RJP")
QBYCC declared and processed
added the following subroutines:
SUBROUTINE BOX27
SUBROUTINE ACTVDEF
SUBROUTINE MKCLUST
SUBROUTINE NBACTV
test/c27test/dynbycc.inp testcase using onefour.22.cls and
top_all22_prot.reor.inp
/data/onefour.22.cls the cluster file
/data/top_all22_prot.reor.inp
reordered the topology file for param 22.
The groups are the same, but the order of the
atoms is different to be consistent with the
cluster file.
------------------------------------------------------------------------------
2.3 Karolinska Institutet Developments and Bugfixes
Name : Lennart Nilsson
Email Address : Lennart.Nilsson@csb.ki.se
Institution : Karolinska Institutet, Sweden
Date : October 7, 1998
2.3.1 install.com for GNU systems
The large variety of fortran compilers available for GNU systems has
created a small mess of the install.com and Makefile_gnu. A simpler scheme
(which also does not upset the linecount in the Makefile) is to keep all
the options in the Makefile and just have install.com uncomment the
appropriate line(s).
Files modified:
install.com
build/UNX/Makefile_gnu
2.3.2 RMS of Interatomic Distances
The option to have the distance matrix command compute the RMSF of
the interatomic distances is added by Ansuman Lahiri(postdoc in the lab).
Files modified:
source/manip/corman2.src
doc/corman.doc
2.3.3 Solana Enhancements
(1) Command syntax is simplified (old syntax still works) with some
redundant keywords made optional.
(2) g(r) is corrected for excluded volume effects.
(3) Option to exclude distances within same group/residue/segment for
radial distribution functions is added.
(4) MSD calculation is made possible for molecules within specific shell
of a site.
Files modified:
source/correl/solana.src
/manip/corman.src
test/c27test/solanal2.inp
doc/corman.doc
2.3.4 Crystal Trajectory Merge
When merging trajectories from a crystal simulation the lattice data
records are not written to the output trajectory unless the crystal has
been setup before the merge operation. A warning about this is added
in subroutine merge. A note is also added in the merge documentation.
Files modified:
source/dynamc/dynsub.src
doc/dynamc.doc
2.3.5 Bugfixes and Minor Changes
(1) Modified PSF Check
If the PSF is modified after images have been defined the image lists
may get screwed up without the user noticing. A check for this is done
in modpsf.src
File modfiied: source/gener/modpsf.src
(2) MALLOC Declaration
Included external declaration of malloc for ALPHA systems in space.src
File modified: source/machdep/space.src
(3) impnon.fcm
ALPHA is added in impnon.fcm
File modified: source/fcm/impnon.fcm
(4) Documentation Update
The link to COOR HBONd is added at the PRINT HBOND section of io.doc.
Files modified: doc/io.doc
------------------------------------------------------------------------------
2.4 Multi-Body Dynamics Code Update
Name : Ryszard Czerminski, Robert Nagle, Eric Koinstine,
Hon Chun and Kim Blair
Email Address : ryszard@moldyn.com
Institution : Moldyn, Inc.
Date : January 25, 1999
This update includes MBO(N)D port to Intel/PPro/Linux, IBM R6000,
HP-UX, and DEC Alpha platforms. Note that we used g77/egcs-1.1a
(from http://egcs.cygnus.com) under Linux on Inter/PPro platforms.
BLAS for Linux/PPro is obtained from http://www.cs.utk.edu/~ghenry/distrib.
Files modified:
install.com sgi64 machine added to allow co-existence
of sgi and sgi64 libraries and executables
build/UNX/Makefile_hpux MBONDFLG introduced, -lblas added; CPP added
/UNX/Makefile_gnu
/UNX/Makefile_ibmrs
/UNX/Makefile_sgi
/UNX/Makefile_sgi64
/UNX/charmm.mk g77 requires .F file if there are cpp directives
/UNX/mbond.mk
/UNX/moldyn.mk
source/fcm/mbmts.fcm MBMTSLEN increased to 64
/adumb/eval.src format change: ...,X,... -> ...,1X,...;
/adumb/umb.src M. Schaefer Bug fix
format change: ...,X,... -> ...,1X,...;
order change from to
real*8 A(N) integer N
integer N real*8 A(N)
/image/xtlfrq.src DCMPLX changed to CMPLX, DIMAG changed to AIMAG
/mbond/mbdiag.src introduced BdyModes_dim for gnu port
/mbond/mbdyn.src MBMTSLEN has to be equal to LENENT
/mbond/mbmodes.src pDELOCAL replaced with qDELOCAL(NBODY)
HEAP(PrpPtr(1)) replaced with
RETVAL8(HEAP(PrpPtr(1)))
ALPHA & DEC ports
/mbond/mbmts.src write(outu,*) replaced with fixed format
/mbond/mbond.src default for MODES HARM added
/mbond/mbutil.src test for empty psf
/mbond/modtrans.src static allocation for gnu introduced
/dynamc/dcntrl.src VVERL not supported in MBOND
/io/parmio.src M. Schaefer Bug fix
/machdep/cstuff.c floating point error trap introduced for gnu
/misc/nmr.src DCMPLX changed to CMPLX
/misc/ssbp.src DCMPLX changed to CMPLX, DIMAG changed to AIMAG
/nbonds/exelec.src DCMPLX changed to CMPLX, DIMAG changed to AIMAG
/nbonds/ace.src Format modification
Reason for this format modification is that some
machines put extra blanks at the end of the line
and some don't therefore it is better to
have 3X,5(2X,G12.3) instead of 5X,5(G12.3,2X)
/nbonds/nbutil.src M. Schaefer Bug fix
/moldyn/ many changes for gnu port...
------------------------------------------------------------------------------
2.5 Bugfixes
(1) ACE parameter setup corrected (B981021.ms1)
source/io/parmio.src
source/nbonds/nbutil.src
(2) Use ZERO for the MIN/MAX function (B981021.ms2)
source/adumb/umb.src
(3) RTF dimension increase (B981024.adm)
source/fcm/dimens.fcm
(4) top_all22_na error fixed (B981025.adm)
toppar/top_all27_na.rtf
line 774 deleted: BOND O4' C1' O4' C4'
(5) LN code with MTS compilation (B981203.ds1)
source/dynamc/dcntrl.src
source/dynamc/dynamln.src
(6) DYNAMLN calling conditional fixed (B981203.ds2)
source/dynamc/dcntrl.src
(7) PBEQ boundary potential correction in the XY plane (B981208.wi)
source/misc/pbeq.src
(8) 4D time series code fixed (B981215.bs Brent T. Speelman)
source/correl/correl.src
(9) testcase update (B981231.ds)
test/c27test/lnx_img.inp
(10) QYT=QYYT*YD+QYZT*ZD+QXYT*XD (B990105.rjp)
source/nbonds/nbondg.src
source/nbonds/nbndgc.src
(11) MBO(N)D code with MTS (B990112.mw)
source/dynamc/dcntrl.src
(12) Testcase and documentation updates (B990112.tl)
doc/eef1.doc
doc/commands.doc
test/c27test/testeef1.inp
(13) MOVE READ command fixed (B990120.ad)
source/mc/moveio.src
The following are introduced and modified during the development period
of February 15, 1999 through August 15, 1999.
3.1 General Hybrid Orbital (GHB) Method
Name : Jiali Gao, Martin Field, Cristobal Alhambra, Patricia Amara
Email Address : jiali@chem.buffalo.edu
Institution : SUNY, Buffalo
Date : June 30, 1999
The generalized hybrid orbital (GHO) method is incorporated into the
semiempirical QM/MM code for treatment of QM-MM boundary. It is an
approach for the treatment of the division across a covalent bond between
the QM and MM region.
The method recognizes a frontier atom, typically carbon which is the
only atom that has its parameters optimized at this time, both as a QM atom
and an MM atom. Thus, standard basis orbitals are assigned to this atom.
These atomic orbitals on the frontier atoms are transformed into a set of
equivalent hybrid orbitals (typically the frontier atom is of sp3
hybridization type). One of the four hybrid orbitals, which points directly
to the direction of the neighboring QM atom, is included in QM-SCF orbital
optimizations, and is an active orbital. The other three hybrid orbitals
are not optimized. Thus, they are the auxillary orbitals.
Since hybridization (contributions from s and p orbitals to the hybrid
orbitals) is dependent on the local geometry, change of bond angles will
lead to bond polarization in the active orbital. Also, since the active
orbital is being optimized in the SCF procedure, charge transfer between
the frontier atom and the QM fragment is allowed. Consequently, the GHO
method provides a convenient way for smooth transition of charge
distribution from the QM region into the MM region.
Files Added:
source/fcm/qlink.fcm
Files Modified:
source/quantum/qmene.src
/quantum/qmjunc.src
/quantum/qmnbnd.src
/quantum/qmset.src
/quantum/qmdata.src
/quantum/qmpac.src
New Documentation:
doc/qmmm.doc
New/Modified Testcase:
test/c28test/but0.inp
/c28test/but1.inp
/c28test/but3.inp
/c28test/but4.inp
/c28test/eth.inp
test/data/BUT.TOPO
/data/ETH.TOPO
/data/QMLANK.PARA
------------------------------------------------------------------------------
3.2 Consistant Force Field Fixes
Name : William S. Young
Email Address : wyoung@msi.com
Institution : MSI
Date : July 1, 1999
The CFF module put into c27a1 has not functioned correctly. Fixes are
made on the following files.
Files Modified:
source/cff/codes_cff.src
/cff/efscalar_cff.src
/cff/enbfast_cff.src
/cff/enbonda_cff.src
/cff/escalar_cff.src
/cff/ewald_cff.src
/cff/parrdr_cff.src
/charmm/iniall.src
/energy/ecntrl.src
/energy/energy.src
/energy/printe.src
/gener/update.src
/io/parmio.src
/manip/cstran.src
/manip/intcor2.src
/mmff/mmff.src
/mmff/readpar.src
/nbonds/enbond.src
/nbonds/nbexcl.src
/fcm/cff.fcm
/fcm/consta.fcm
/fcm/psf.fcm
New Documentation:
doc/cff.doc
New Testcases:
test/ccfftest/cff_rtf.inp
/ccfftest/dyntest1.inp
/ccfftest/makeetoh.inp
/ccfftest/minimize.inp
/data/aminoh_cff.rtf
/data/bdna.crd
/data/bdna.psf
/data/cff93.frc
/data/small_cff.rtf
/data/top_all22_model_cff.inp
------------------------------------------------------------------------------
3.3 TSRI Developments
Name : TSRI - C.L. Brooks, III, M.F. Crowley
Email Address : brooks@scripps.edu, crowley@scripps.edu
Institution : The Scripps Research Institute
Date : July 19, 1999
3.3.1 Fixed problem with install.com that incorrectly dealt with MPI
parallel installation when sgi64 was machine type selected.
Files involved: install.com
3.3.2 Bugfix of declarations in correl/solana.src, image/nbndgcm.src
3.3.3 Reformatted clustst.hex to be consistent with changed formatting of
hex files as of c27.
File involved:
test/data/clustst.hex
3.3.4 Added new options to GBorn module (GBAtm), calculation of atomic
contributions to GBORN energy. Accessible from scalar commands. Also
added support for GB calculations with MMFF and CFF95.
Files Modified:
source/energy/genborn.src
/energy/energy.src
/fcm/genborn.fcm
/manip/scalar.src
doc/genborn.doc
/subst.doc
3.3.5 Added hardcoding of idynpr = 1 for parallel runs to eliminate
hangs when prnlev > 4 for lass than all the nodes.
File Modified:
source/dynamc/dcntrl.src.
3.3.6 IMCUBES (bycb) enhancements for parallel functioning, load balancing,
and memory savings.
Files Modified:
source/charmm/iniall.src
/fcm/deflts.fcm
/fcm/inbnd.fcm
/fcm/image.fcm
/image/images.src
/image/nbndgcm.src
/io/parmio.src
/nbonds/cenbf.src
/nbonds/enbf2.src
/nbonds/enbfast.src
/nbonds/enbond.src
/nbonds/enbonda.src
/nbonds/etable.src
/nbonds/evdwf.src
/nbonds/ewald.src
/nbonds/nbonds.src
/nbonds/nbutil.src
3.3.7 IMCUBES: expanded to work with other methods:
source/cff/enbfast_cff.src
/cff/ewald_cff.src
/energy/genborn.src
/energy/intere.src
/image/xtlfrq.src
/mbond/mbdiag.src
/misc/hbuild.src
/mmff/enbfast_mm.src
/mmff/enbscalar_mm.src
/energy/genborn.src
/image/nbndgcm.src
/nbonds/ace.src
/nbonds/acean.src
/nbonds/cenbf.src
/nbonds/nbonds.src
3.3.8 PME plasma correction for charged systems. Initial stab at this and
the virial might not be correct. Gives consistent answers for any number
of processors, and does not do a second reciprocal sum.
FIle Modifiled:
source/nbonds/pme.src
3.3.9 Added code modification to image/nbndcm.src write statement too long.
3.3.10 Added new testcases for generalized Born and new cubes list:
New testcases:
test/c27test/GB_CFF-data.inp
/c27test/GB_CFF95_na-test.inp
/c27test/GB_CFF95_prot-test.inp
/c27test/GB_MMFF94_prot-test.inp
/c27test/GB_MMFF94_test.inp
/c27test/GB_MMFF94_na-test.inp
/c27test/cubesdyn.inp
/c27test/cubesgb.inp
/c27test/cubesvac.inp
/c27test/cubesxtl.inp
/c27test/genborn19.inp
/c27test/genborn22.inp
/data/1ptq.crd
/data/287d.crd
/data/ade-cyt.crd
/data/ade.crd
/data/aminoh_cff.rtf,
/data/par_all22_na.inp
/data/par_all22_prot.inp
/data/ser-tyr.crd
/data/small_cff.rtf
/data/top_all22_na.inp
/data/top_all22_na_cff.rtf
------------------------------------------------------------------------------
3.4 NIH Developments
Name : Bernard R. Brooks
Email Address : brbrooks@helix.nih.gov
Institution : Computational Biophysics Section
Laboratory of Biophysical Chemistry
National Heart, Lung and Blood Institute
National Institutes of Health
Date : July 19, 1999
3.4.1 New Hbond analysis and manipulation capabilities
These command enhancement makes it easier to modify hbond lists and
to track hbonds as a funtion of time.
New DONOr and ACCEptor commands
[ DONOr ] [ REMOve ] atom-selection [NOANtecedents] [SHOW]
[ ACCeptors] [ ADD ]
[ SET ]
New SCALar HBCOunt command option
SCALar keyname { HBCOunt [atom-selection] } ! A = #of hbonds
Files modified:
source/charmm/charmm_main.src
/gener/hbonds.src
/manip/scalar.src
doc/scalar.doc
..............................................................................
3.4.2 New internal coordinate capabilities and dihedral restraints
These commands facilitate the development of Monte Carlo scripts.
1. New IMPRoper value for all "*" type IC elements.
The old keyword value, DIHE, only refers to normal dihedral IC types.
CONStraint IC [BOND real [EXPOnent integer] [UPPEr]]
[ANGLe real] [DIHEdral real] [IMPRoper real]
2. New COMP and MAIN keywords, allow current dihedral values to be
specified based on current coordinate values.
CONS DIHEdral [BYNUM int int int int] [FORCe real] [MIN real] [PERIod int]
[WIDTh real]
[ atom-selection ] [ COMP ]
[ 4X(atom-spec) ] [ MAIN ]
3. New OVERwrite option added IC SAVE and IC RESTore commands to
assist MC script design.
IC { SAVE [PREServe ] }
{ RESTore [OVERwrite] }
Files modified:
source/charmm/iniall.src
/fcm/cnst.fcm
/io/mainio.src
/manip/cstran.src
/manip/intcor.src
doc/miscom.doc
/intcor.doc
/cons.doc
..............................................................................
3.4.3 Flat bottom dihedral restraints
This command option improves the ability to determine structures with NMR
restraints.
A WIDTh value is added to the CONS DIHE command which allows a flat
bottom restraint. The default value is zero, so current scripts will
work as before.
CONS DIHEdral [BYNUM int int int int] [FORCe real] [MIN real] [PERIod int]
[WIDTh real]
[ atom-selection ] [ COMP ]
[ 4X(atom-spec) ] [ MAIN ]
This required changing the calling sequence to EPHI, so lots of files
are modified.
Files modified:
source/correl/anacor.src
/energy/ecnstr.src
/energy/ecntrl.src
/energy/ediff.src
/energy/eintern.src
/energy/energy.src
/energy/intere.src
/fcm/cnst.fcm
/fcm/pert.fcm
/image/eimage.src
/io/mainio.src
/manip/cstran.src
/mbond/mbdiag.src
/mc/mcener.src
/misc/genetic.src
/misc/hbuild.src
/misc/testch.src
/pert/epert.src
/pert/icfcnf.src
/pert/icpert.src
/pert/pert.src
/pert/tsme.src
doc/cons.doc
..............................................................................
3.4.4 Arguments on the STREam command
The STREam command has been extended to allow arguments.
The command;
STREam filename arg1 arg2 arg3 arg4
is functionally equivalent to;
SET IN1 arg1
SET IN2 arg2
SET IN3 arg3
SET IN4 arg4
STREam filename
This simplifies the use of passed parameters to a stream file.
Files modified:
source/charmm/miscom.src
..............................................................................
3.4.5 Changes needed to support REPLICA/PATH enhancements
The ROTLSQ procedure (least squares best fit) has been modified
so that it can handle degenerate eigenvalues with no force
discontinuity when this method is used with harmonic restraints.
A width parameter (EVWID) which kicks in a switching function
region between solutions when eigenvalues are below this tolerance.
The code has been simplified in places.
The free energy path code using REPLICA/PATH with MD is still in
development and is only partially presented here.
Files modified:
source/energy/ecnstr.src
/energy/epath.src
/fcm/path.fcm
/manip/rotlsq.src
doc/replica.doc
..............................................................................
3.4.6 Bugs and/or Problems Fixed
(1) Fix ##IF boundary usage
The location/presence of ##IF statements has been modified to correct
code deficiencies.
Files modified:
source/dynamc/dcntrl.src
/dynamc/dynsub.src
(2) Added a warning if PSF is modified after images is setup.
Files modified:
source/gener/modpsf.src
(3) Input and output files now required for DYNUFO. Bug fix in use of
energy array length.
Files modified:
source/dynamc/dynio.src
(4) Replace CMPLX with DCMPLX: revert to past usage and let preflx sort it out
Files modified:
source/image/xtlfrq.src
/misc/nmr.src
/misc/ssbp.src
/nbonds/exelec.src
(5) Spelling fixes and removal of unwanted blank lines (e.g. at end of file).
Files modified:
source/dynamc/trnphi.src
/nbonds/nbndcc.src
(6) Changes for the Y2K problem
Files modified:
machdep/machutil.src
(7) Fix calling sequence problems: Subroutine SQUAREUP and Subroutine SAVGD1
had problems (untested changes).
Files modified:
source/manip/corman3.src
/misc/pbeq.src
..............................................................................
3,4,7 Documentation Updates
Additional documentation to clarify command usage and sequence.
In some cases, fix things that are wrong (e.g. RMSD command). Also, add
documentation that was missing from previous NIH code release (correl.doc)
and missing from other added code (new COEFf options missing in block.doc).
Files modified:
doc/block.doc
/correl.doc
/crystl.doc
/dynamc.doc
/io.doc
/miscom.doc
/select.doc
..............................................................................
3.4.8 New graphics code and graphics overhaul by Rick Venable
- Rick_Venable@nih.gov (FDA/CBER Biophysics Lab)
It's a wholesale rennovation of the graphics code, removing Apollo and
GL support, adding the POV-Ray interface (another output file type),
and several bugfixes and minor feature additions.
install.com is modified to remove the GL support option, which is
replaced with support for the NODISPLAY keyword, which allows producing
graphics output files w/o any kind of screen display.
New files:
source/graphics/povdfn.src
Deleted files:
source/graphics/iris_graphics.c
/graphics/ugap.src
/graphics/inter.src
------------------------------------------------------------------------------
3.5 Moldyn Code Updates
Name : Ryszard Czerminski, Masa Watanabe, Hon Chun, Eric Koistinen
Donovan Chin
Email Address : {ryszard,watanabe,hon,koistine,dnc}@moldyn.com
Institution : Moldyn, Inc.
Date : July 29, 1999
Detailed description of fixes per each file:
build/UNX/Makefile_sgi64
INCLUDE = -I ../../source/moldyn added to avoid links
build/UNX/charmm.mk
mw: mbmts1.fcm added,
rc: param_mbond.fcm replaced by PARAM.FOR to avoid links
build/UNX/moldyn.mk
hc: missing dependencies added
install.com
ek: null_moldyn.mk removed; if NOGRAPHICS in pref.dat exclude graphics.a
source/charmm/charmm_main.src
ek: call to graphics put under ##IFN NOGRAPHICS
source/charmm/iniall.src
mw: mbmts modifications
source/correl/solana.src
rc: SAVE NCONF,NPCHK... removed (duplicated variables)
source/dynamc/dynio.src
ILENET replaced by ILENEP:f
# (from Lennart.Nilsson@csb.ki.se)
source/energy/energy.src
mw: mbmts modifications
source/fcm/mbmts.fcm
mw: mbmts modifications
source/mbond/mbmts.src
mw: mbmts modifications
source/mbond/mbond.src
mw: 0. replaced by ZERO in GTRMF
source/mbond/mbsub.src
mw: mbmts modifications
source/minmiz/egrad1.src
dc: pass values of XUCELL with CALL SETMSR
source/moldyn/ctinit1_CHARMM.f
source/moldyn/extor_CHARMM.f
source/moldyn/lobto4.f
source/moldyn/mbdyna.f
source/moldyn/mbtopol.f
source/moldyn/mdloop_CHARMM.f
source/moldyn/mtsratio.f
source/moldyn/prntbd.f
source/moldyn/prnten.f
source/moldyn/prntsm.f
source/moldyn/rotdh1_CHARMM.f
source/moldyn/ydot.f
hc: CALL ROTDS replaced by CALL ROTDS_1
source/nbonds/enbfast.src
mw: mbmts modifications
source/nbonds/exelec.src
DIMAG replaced with generic AIMAG
source/nbonds/nbonda.src
mw: mbmts modifications
Files Added:
source/fcm/mbmts1.fcm
/fcm/HANDS2.INC ! copied from source/moldyn/
/fcm/HEAPMB.INC ! Note that Symbolic links in source/fcm/
/fcm/IFIRST.INC ! are no longer needed
/fcm/INTGRL.INC !
/fcm/PARAM.FOR !
/fcm/SPECIF.INC !
Files Removed:
source/moldyn/VDBUG.INC
/mbond/nul_mdyn.src
------------------------------------------------------------------------------
3.6 INTE with GROUP and EEF1, EEF1 with images
Name : Themis Lazaridis
Email Address : themis@sci.ccny.cuny.edu
Institution : City College of New York
Date : June 17, 1999
1) Allowing INTE command to work with GROUP by adding subroutine INTER3G
in intere.src
2) Including the EEF1 solvation free energy in INTE by adding a call to
EEF1EN in subroutine INTER2 and a slight modification of EEF1EN
3) Making EEF1 work with images: small changes in EEF1EN and addition of
subroutine EEF1IM in eef1.src
Files Modified:
source/misc/eef1.src
/energy/energy.src
/energy/intere.src
/image/upimag.src
/fcm/eef1.fcm
Modified Documentation:
doc/eef1.doc
/energy.doc
Modified Testcase:
test/c27test/testeef1.inp
New Testcase:
test/c27test/testeef1imag.inp
test/data/testeef1imag.crd
------------------------------------------------------------------------------
3.7 BYCC Modifications
Name : Robert J. Petrella
Email Address : petrella@tammy.harvard.edu
Institution : Harvard University
Date : July 21, 1999
Files Modified:
source/fcm/actclus.fcm
/fcm/exclar.fcm
/nbonds/nbutil.src
/nbonds/nbndcc.src
/nbonds/nbexcl.src
/manip/corman3
doc/nbonds.doc
------------------------------------------------------------------------------
3.8 A variety of small improvements to the MC module.
Name : Aaron R. Dinner
Email Address : dinner@tammy.harvard.edu
Institution : Harvard University
Date : July 12, 1999
(1) MOVE ADD now stores the number of move instances in the substitution
variable ?NMVI.
(2) Rotations of rigid bodies are allowed around their centers of mass in
addition to selected atoms.
(3) The EEF1 term is now included in the MC energy.
(4) Better handling when the multicanonical MC simulations creep out of
the allowed window of energies.
(5) Bugfixes in mvdihe.src
Files Modified:
source/mc/mc.src
/mc/mvdihe.src
/mc/mcener.src
/mc/movead.src
/mc/mvrtrn.src
Modified Documentation:
doc/mc.doc
------------------------------------------------------------------------------
3.9 Bugfixes
(1) Error in calculation if group is its own image (B990329.ds)
Name : Dan Strahs, Tamar Schlick
Email Address : strahs@winestock.biomath.nyu.edu
Institution : Dept. of Chemistry, NYU/HHMI
Date : Mar. 29, 1999
At the point when the MKIMAT subroutine examined a transformed group
to see if it was its own image, the X variable for the original position
of the group center was erroneously used for Y and Z positions.
Files involved:
source/image/upimag.src
..............................................................................
(2) c27 does not read old restart files (B990330.ln)
Name : Lennart Nilsson
Email Address : Lennart.Nilsson@csb.ki.se
Institution : Karolinska institutet, Center for Structural Biochemistry
Date : March 30, 1999
In routine READYN the wrong conunter, ILENET instead of ILENEP,
is used on line 1378
Files involved:
source/dynamc/dynio.src
..............................................................................
(3) MTS specific variable not encapsulated by ##IF MTS (B990426.ds)
Name : Dan Strahs, Tamar Schlick
Email Address : strahs@winestock.biomath.nyu.edu
Institution : Dept. of Chemistry, NYU
Date : Apr. 26, 1999
The logical variable QLNX is used to call the LN integrator, a multiple
time-step integrator. There was a use of QLNX not bracketed by
##IF MTS ... ##ENDIF
Files involved:
source/dynamc/dcntrl.src
..............................................................................
(4) exponential of too large a number causes core dump (B990727.mc)
Name : Michael F. Crowley
Email Address : crowley@scripps.edu
Institution : Scripps
Date : 27 Jul 1999
either core dump or very bad answers occur when argument of exp in:
DMSTATE=ONE/(ONE+EXP(TWENTY*(DIST-(DMCUT+PT25)))) !"EXP"?
gets too large for that function to produce a valid float number.
checking is added to solve the problem so that DMSTATE is set to
ZERO when the argumet gets large enough.
Files involved:
source/energy/dmcons.src
The following are introduced and modified during the development period
of August 15, 1999 through February 15, 2000.
4.1 TSRI Fixes and Enhancements
Name : Charles L. Brooks, III, Michael F. Crowley
Email Address : brooks@scripps.edu, crowley@scripps.edu
Institution : The Scripps Research Institute
Date : January 15, 2000
4.1.1 Compilation Enhancement
MPI installation procedures are reworked to modify machine specific
Makefiles. Makefile_gnu is modified for pgf compiler and g77 compilation
options are added to increase performace by ~100%. The optimization level
is altered in nbondg.src compilation for Linux PGI compiler.
Files modified:
install.com
build/UNX/Makefile_cspp
/Makefile_gnu
/nbonds.mk
4.1.2 Documentation Update
Rg/RMSD restraint and Distance Matrix restraint are documnented.
File Modified:
doc/cons.doc
4.1.3 Memory Save and Bugfixes
plnod0 (prnlev node 0) is added and broadcasted to other nodes.
Changes are for saving memory, readcv bugfix, initializing variables.
A bug is fixed in stream file handling.
Files Modified:
source/charmm/miscom.src
/correl/anacor.src
/solana.src
/dynamc/dcntrl.src
/dynio.src
/dynsub.src
/trnphi.src
/energy/eintern.src
/fcm/heap.fcm
/parallel.fcm
/gener/genpsf.src
/image/nbndgcm.src
/io/psfres.src
/rtfio.src
/trajio.src
/machdep/paral1.src
/manip/corman2.src
/cstran.src
/dynanal.src
/hbanal.src
/intcor.src
/minmiz/abner.src
/misc/hbuild.src (Milan's parallel bugfix)
/nmr.src (NO_DQS addded)
/sbound.src
/nbonds/nbndcc.src
/nbonds.src
/nbutil.src
/pert/block.src
/icfcnf.src
/rxncor/travel.src
/vibran/quasi.src
/rbquas.src
4.1.4 Parallel Generalized Born Model Code
RMSD-based extension of Rg restraint is added. Parallel gb is fixed
and clean up the code.
Files Modified:
source/energy/energy.src
/genborn.src
/intere.src
/rgy.src
/fcm/rgy.fcm
4.1.5 Cray T3E Related Modifications
LBYCBIM flag is added in calling parameters. NO_BYCU is fixed.
Protected PME_PLAMSA code for non parallel compile. Trajectory
format/unformat is fixed.
Files Modified:
source/nbonds/cenbf.src
/nbndgc.src
/pme.src
/util/util.src
4.1.6 Testcase Fixes
Unit number 99 conflicts with an internal file open unit number,
changed to 89. And other problems causing crash are fixed
Files Modified:
test/c20test/dyntest1.inp
/quasi.inp
/c22test/stdtest.inp
/c25test/hba1.inp
/c26test/pathint.inp
/c27test/mbtest30.inp
------------------------------------------------------------------------------
4.2 MBO(N)D Updates
Name : Masa Watanabe
Email Address : watanabe@moldyn.com
Institution : Moldyn, Inc.
Date : December 23, 1999
4.2.1 MOLDYN Include Files
Modifications of MBO(N)D are not correctly implemented in c27b1 and
c28a1. The following include files should be located in two places
source/fcm and source/moldyn. Both places should have exactly the same
files. In c27b1 and c28a1, only source/fcm has the correct version of
these files. Copy source/fcm include files into source/moldyn.
Files involved:
source/moldyn/HANDS2.INC
/HEAPMB.INC
/IFIRST.INC
/INTGRL.INC
/PARAM.FOR
4.2.2 MBO(N)D Fixes and Enhancements
MBO(N)D related bugs have been fixed and BLAS Library dependent code has
been eliminated. MBO(N)D documentation has been updated. c25test/mtsm3.inp
is updated to use atom based cutoff.
Files modified:
build/UNX/Makefile_gnu
/Makefile_sgi
/Makefile_sgi64
/Makefile_ibmrs
source/fcm/mbond.fcm
/mbond/mbdiag.src
/mbmodes.src
/mbond.src
/mbutil.src
/modtrans.src
doc/mbond.doc
test/c25test/mtsm3.inp
The following are introduced and modified during the development period
of February 15, 2000 through August 15, 2000.
4.1 TSRI Fixes
Name : Charles L. Brooks, III, Michael F. Crowley
Email Address : brooks@scripps.edu, crowley@scripps.edu
Institution : The Scripps Research Institute
Date : April 11, 2000
(1) source/correl/solana.src
RHOMIN is initialized to compile the code. Should be checked.
IOLEV control added.
(2) source/machdep/paral1.src
mpif.h is included for IBMSP
(3) source/nbonds/pme.src
Variables IGOOD, KBOT, and KTOP are added to the GRAD_SUM call.
(4) source/nbonds/pmeutil.src
mpif.h is included for IBMSP
STATUS call is fixed for IBMSP
(5) source/quantum/qmpac.src
Variables ETA and EPS are saved.
..............................................................................
4.2 Harvard Fixes
Name : Aaron R. Dinner
Email Address : dinner@tammy.harvard.edu
Institution : Harvard University
Date : June 21, 2000
(1) SKIP NONE
SKIP NONE turns off QM electrostatic terms.
Correct QEQTRM(I) = SKIP to QEQTRM(I) = SKIPN.
Files involved:
source/energy/eutil.src
(2) QM/MM VDW energy calculations
QM/MM VDW energies vary with machine due to failure to update group
centers in some cases. A logical variable is passed to an integer argument
(LCENTR) of EGROUP, which results in a machine-dependent cast.
Files involved:
source/quantum/qmene.src
(3) Program hangs during first energy calculation
GNU preprocessor options concerning QMMMDATA should be the same as
ALPHA/IRIS/DEC rather than OS2/HPUX. Local variables are not properly
initialized. Add the compiler flag '-finit-local-zero -fno-automatic' to
the FC0 macro.
Files involved:
source/quantum/qmdata.src, quantum/qmset.src
build/UNX/Makefile_gnu
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6. c27b4 Change Log |
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The following are introduced and modified during the development period
of August 15, 2000 through February 15, 2001.
6.1 TSRI Fixes and Enhancements
Name : Charles L. Brooks, III and Michael F. Crowley
Email Address : brooks@scripps.edu, crowley@scripps.edu
Institution : The Scripps Research Institute
Date : December 29, 2000
1) IC SEED Atom specification added
Files involved:
doc/galgor.doc
source/fcm/galgor.fcm
/misc/genetic.src
2) Softcore potential is active on multiple energy calls without
respecification.
Files Involved:
source/nbonds/nbutil.src