ChangeLog.c34
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CHARMM 34 |
| c34a1 |
Developmental |
August 15, 2006 |
| c34a2 |
Developmental |
February 15, 2007 |
| c34b1 |
Release |
August 15, 2007 |
| c34b2 |
Release |
February 15, 2008 |
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About CHARMM34 Development |
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At the July 2006 CHARMM meeting (Harvard University, July 21-23, 2006),
we decided to release CHARMM c33b1 with incorporating enhancements and fixes
to the developmental version c33a2. The modified source code and features
are described in ChangeLog.c33, [3] c33b1 Change Log.
As an on-going project, CHARMM development will be carried out
with CHARMM version 34a series. The following describes new features
and enhancements incorporated in the c34 development period.
The following are introduced and modified during the development period
of February 15, 2006 through August 15, 2006. The developments are
based on CHARMM version c32a2. Some enhancements and fixes to c33a2
are also incorporated into c33b1 as described in the c33b1 release note
(ChangeLog.c33).
1.1 TSRI Developments
Developers : Mike Crowley, Jianhan Chen, Wonpil Im,
Charles L. Brooks, III
Email Address : crowley@sripps.edu, brooks@scripps.edu
Institution : The Scripps Research Institute
Date : July 10, 2006
1.1.1 Faster code constructs introduced into ewald.src
Ewald code has been much slower than other programs. New code constructs
with the ability to use vector libs for speed has been added as well as
rearrangement of loops to aid compiler optimization. Minimal implementation
in this version: constant volume (no pressure code), vswitch only, faster 1
only (not faster or faster on) so that ewald.src is used and not the new faster
routines. So far this is significantly faster than the expand faster routines
but if it is accepted as valid, can be migrated into the expand routines or
expand can be applied to this routine
Pref keyword: FEWMFC (Faster EWald mfc)
Files Modified:
source/nbonds/ewald.src
..............................................................................
1.1.2 Torsion Angle Molecular Dynamics (TAMD)
Carry out molecular dynamics and energy minimization in torsional space
using atomic forces in Cartesian space. Current verson only support a single
continuous peptide chain. Associated internal cooridinate force field is built
from CHARMM22 with CMAP cross-term corrections to suppress distortions of the
potential energy surface due to rigid convalent geometry.
Files Added:
source/dynamc/tamd.src
toppar/tamdfff/top_all22_prot_cmap.ahbb4.inp
toppar/tamdfff/par_all22_prot_tadcmap.ahbb4.inp
toppar/tamdfff/par_tadmap.chi1.ahbb4.inp
Files Modified:
source/charmm/initall.src
source/charmm/charmm_main.src
source/fcm/dimens.fcm
New Documentation:
doc/tamd.doc
New Testcase:
test/c34test/tamd_ala10.inp
..............................................................................
1.1.3 Periodic boundary list builder with no image atoms
Periodic boundary conditions are simulated without image atoms for the
purposes of speeding up large simulations where the updating of image atoms
can be very expensive. This only works at present with constant volume
simulations and only for simple periodic boundary systems where the full unit
cell is represented, does not work for general imaging or assymetric units.
This feature is currently implemented for ewald via the ewald.src
implementation (faster 1). It is included for testing purposes and will be
generalized if it is found useful.
It must be compiled without IMCUBES since some of the entries in data
structures are re-used. Specify "bypb" as a nonbond keyword in nonbond,
energy, and dynamics commands.
Pref.dat keyword: PBCUBES
Files Removed:
source/fcm/pbcubes.fcm
Files Modified:
source/cff/enbfast_cff.src
source/ewald_cff.src
source/charmm/iniall.src
source/energy/energy.src
source/energy/gbim.src
source/energy/gbmv.src
source/energy/genborn.src
source/fcm/inbnd.fcm
source/gener/update.src
source/image/upimage.src
source/image/xtlfrq.src
source/misc/hbuild.src
source/nbonds/ace.src
source/nbonds/enbfast.src
source/nbonds/enbond.src
source/nbonds/ewald.src
source/nbonds/heurist.src
source/nbonds/nbonds.src
source/nbonds/nbutil.src
source/nbonds/pblist.src
..............................................................................
1.1.4 GBMV modernized a bit and fast bug fixed
GBMV module added to start modernization of GBMV code and simplify
debugging process. GBMV fast fixed
Files Added:
source/energy/gbmvmodule.src
Files Modified:
source/charmm/charmm_main.src
source/energy/energy.src
source/energy/gbmv.src
source/energy/intere.src
source/fcm/gbmv.fcm
..............................................................................
1.1.5 Numerous fixed and modifications
- Compiler upgrades in the makefiles and install.com
- Testendian minor fix
- Ability to read psf's with CHEQ information with executable without CHEQ
- Flush for xlf compilers
- Include file specs for mpif.h fixed and enhanced
- Excess output from parallel runs with fast shake fixed
- Fixed use of noninteger loop indices and incorrect array indices
- Timer formatting changed to allow very long times to be printed
- Preprocessor fix for gfortran compiles
- Missing CMAP entry for HSP in toppar/top_all22_prot_cmap.inp
Files Modified:
install.com
build/UNX/Makefile_gnu
build/UNX/Makefile_osx
source/dynamc/dynio.src
source/energy/ecnstr.src
source/fcm/path.fcm
source/fcm/pme.fcm
source/io/psfres.src
source/machdep/machio.src
source/machdep/paral1.src
source/machdep/startup.src
source/manip/fsshake.src
source/manip/shake.src
source/manip/secstr.src
source/minmiz/minmiz.src
source/minmiz/steepd.src
source/misc/quicka.src
source/nbonds/nbutil.src
source/nbonds/pmeutil.src
source/quantum/mpiqub.src
source/util/new_timer.src
source/util/string.src
tool/preflx
toppar/top_all22_prot_cmap.inp
------------------------------------------------------------------------------
1.2 GBMV Improvements
Developer: : Seiichiro Tanizaki, Michael Feig
Email Address : feig@msu.edu
Institution : Michigan State University
Date : June 30, 2006
Spatial variation of atomic radii in heterogeneous dielectric model is
implemented. Van der Waals dispersion term is added to GBMV according to
E. Gallicchio and RM Levy, J Comput Chem 25: 479--499, 2004. Spherical and
cylindrical heterogeneous dielectric environments are also added.
Files Modified:
source/energy/gbmv.src
source/fcm/gbmv.fcm
source/energy/energy.src
Modified Documentation:
doc/gbmv.doc
New Testcases:
test/c34test/gbmv_vdw.inp
test/c34test/hdgb_corr3.inp
test/c34test/hdgb_corr4.inp
test/c34test/hdgb_corr5.inp
------------------------------------------------------------------------------
1.3 Developments at University of Chicago (Benoit Roux)
Developers : Edward Harder, Hyung-June Woo,
Nilesh Banavali, Yuqing Deng, Benoit Roux
Email Address : edh2004@med.cornell.edu, woo@unr.edu,
banavali@uchicago.edu, roux@uchicago.edu
Institution : Weill Cornell Medical College
Date : June 27, 2005
1.3.1 Anisotropic Drude Spring
To make the local polarization response around a drude oscillator
anisotropic an additional energy term (called with the ANISOTROPY flag) is
added to modify the components of the Drude force constant tensor.
Files Added:
source/fcm/aniso.fcm
Files Modified:
source/charmm/charmm_main.src
source/charmm/iniall.src
source/energy/energy.src
source/gener/drude.src
source/pert/epert.src
..............................................................................
1.3.2 Constrained RMSD Enhancements
The flat bottom potential has been added to the force-const-spect as
specified by the keyword BOFFset in force-const-spec of the CONS command.
The potential functional form is
E = Sum_i KFORCE_i * [Abs(RMSD - OFFSET_i) - BOFFset_i]**2
if Abs(RMSD-OFFSET_i) > BOFFset_i and zero otherwise, where RMSD is either
the single RMSD, or RMSD(Main)-RMSD(COMP) with the RELAtive keyword.
The BOFFset keyword is the bottom offset distance (default: 0.0).
The dynamic memory allocation requirement has been improved. The memory
is now allocated for a pre-declared maximum "number" of rmsd constraints,
specified by the keyword MAXNrmsd (default: 10), which replaces the
MAXRmsd (maximum number of atoms constrained) of the previous implementation.
A warning message is added to indicate the change if MAXRMSD is invoked in
input file. The code WRNDIEs if CONS RMSD is invoked more than MAXN times
without CONS RMSD RESEt (One RELAtive constraint counts twice). The actual
memory spaces for atoms are allocated dynamically within the atom SELEction
parts of each CONS RMSD commands.
The zeta potential added in CHARMM32 is commented out since it fails
TEST FIRST.
Files Modified:
source/fcm/rmsd.fcm
source/energy/ecnstr.src
source/energy/rmsd.src
source/manip/cstran.src
New Testcase:
test/c33test/test_rmsd3.inp
..............................................................................
1.3.3 PDB File I/O Enhancements
Added the option OFFI to pdb read and write. The OFFI option enforces
the segid to be one character in length.
Files Modified:
source/io/coorio.src
Modified Documentation:
doc/io.doc
..............................................................................
1.3.4 GSBP and SSBP Warning Messages
Added warning messages if the nonbond interaction options are not
compatible with GSBP and SSBP. Added a steep potential in the GSBP
cavity potential at the GSBP boundary to prevent atoms from escaping
the simulation sphere.
Files Modified:
source/fcm/ssbp.fcm
source/machdep/ensemble.src
source/misc/gsbp.src
source/misc/nmr.src
source/misc/fitcharge.src
source/nbonds/nbutil.src
..............................................................................
1.3.5 DYNAMVV2 Bugfix
"floating point exception error" when running the dynamvv2 integrator
on alpha machines is fixed by initializing HEAP(XNEW).
Files involved:
source/dynamc/dcntrl.src
------------------------------------------------------------------------------
1.4 University of Chicago Developments
Developers : Jie Hu, Ao Ma, Aaron R. Dinner
Email Address : dinner@uchicago.edu
Institution : The University of Chicago
Date : June 30, 2006
1.4.1 Steered Molecular Dynamics (SMD)
Implemented a steered molecular dynamics through RXNCOR and integrated
it with transition path sampling (TPS) to allow generation of reactive
trajectories de novo (see Hu, J., Ma, A. and Dinner, A. R., J. Chem. Phys.,
submitted). The SMD can be used without TPS. Symmetric (harmonic) biasing
potentials are advanced in a ratchet-like manner.
Files Added:
source/rxncor/smd.src
Files Modified:
source/dynamc/tps.src
source/fcm/rxncom.fcm
source/rxncor/rxndef.src
source/rxncor/rxnene.src
Modified Documentation:
doc/umbrel.doc
doc/tps.doc
..............................................................................
1.4.2 Periodic Reaction Coordinates
The RXNCOR module is extended such that biasing potentials can be
applied to periodic reaction coordinates. A keyword PERIod is added to specify
the period of the order parameter (default is zero). The SMD code and TPS
are updated to allow basins to span the transition from hi to low values.
Files Modified:
source/dynamc/tps.src
source/fcm/rxncom.fcm
source/rxncor/rxndef.src
source/rxncor/rxnene.src
source/rxncor/smd.src
Modified Documentation:
doc/umbrel.doc
..............................................................................
1.4.3 Vector Option for RXNCOR
A vector analog of SCOMbination, VCOMbination option is added for RXNCOR.
Geometric elements such as points, lines and planes to which biasing potentials
are applied can be defined in terms of not only single atoms but also the
weighted mean of selected coordinates.
Files Modified:
source/fcm/rxncom.fcm
source/rxncor/rxndef.src
source/rxncor/rxnene.src
Modified Documentation:
doc/umbrel.doc
..............................................................................
1.4.4 TPS Enhancements
Allowed TPS to read shorter trajectories into longer ones in order to
lengthen the allowed transition time. A keyword PNSAve is added to specify
the number of phase points in the short trajectories (default is the number
of phase points to be saved in the new trajectories).
Files Modified:
source/dynamc/dcntrl.src
source/dynamc/tps.src
..............................................................................
1.4.5 The Wang-Landau Sampling Method in MC
See Ma, A., Nag, A. and Dinner, A. R., J. Chem. Phys., 124, 144911 (2006)
for an application of the code and references on the method.
Files Added:
source/mc/wl.src
Files Modified:
source/mc/mc.src
Modified Documentation:
doc/mc.doc
New Testcase:
test/c34test/wl_test.inp
..............................................................................
1.4.6 PERT Support in MC
Collaborated with Yuqing Deng(deng@mcs.anl.gov) and
Benoit Roux (roux@uchicago.edu)
The modifications make MC and PERT module compatible for atom-based
nonbond energy evaluations. When PERT is activiated, the MC module constructs
two additional symmetric nonbond lists for the reactants and products. The
orginal nonbond list is used for the environment (the interactions that do
not change with lambda, the control variable). When PERT is active, the
nonbond interaction energy is (1-lambda)*E_react + lambda*E_prod + E_env.
MC-PERT works with GCMC and GSBP but not images.
Files Modified (module/file.src):
source/mc/mc.src
source/mc/mcener.src
source/mc/mvgcmc.src
Modified Documentation:
doc/mc.doc
Modified Testcase:
test/c34test/pert_gsbp_gcmc.inp
..............................................................................
1.4.7 Bugfixes
(1) Transition Path Sampling (TPS) crashes when run in parallel
Two specific problems contribute: (1) The MAIN and COMParison coordinate
sets are not syncrhonized prior to calling TPSUPD and (2) selection of the
phase space point for shooting is not restricted to the master node.
- MAIN XYZ replace COMP in TPSUPD call (dynamc.src).
- Random seed is broadcast to force identical operation of nodes (dcntrl.src).
Files involved:
source/dynamc/dcntrl.src
source/dynamc/dynamc.src
(2) Failure to de-reference pointer to the FREEAT array in TPSWRI call.
FREEAT replaced with STACK(FREEAT) in TPSWRI call.
Files involved:
source/dynamc/dcntrl.src
(3) GC arrays are not properly updated following global moves such as
HMC and MC-minimization. GCMCUP call is forced after acceptance of a global
move.
Files involved:
source/mc/mc.src
------------------------------------------------------------------------------
1.5 Developments at University of Vienna
Developers : Tibor Rudas, Stefan Boresch and Othmar Steinhauser
Email Address : tibi@mdy.univie.ac.at, stefan@mdy.univie.ac.at
Institution : University of Vienna
Date : June 30, 2006
1.5.1 Solvent-related Correlation Functions
CORSOL calculates correlation functions similar to CORREL, but is
optimized for handling solvent related properties. Specifically, CORSOL
handles the averaging over, e.g., all waters in the system. For each trajectory
frame evaluated, SHELL information is updated (if required) and can be used by
CORSOL. In fact, one of the primary applications of CORSOL is to compute time
series and correlation series based on the binary indicator function N(t) = 1
or 0, depending whether a molecule is in a particular shell at time t or not.
Currently the following series are implemented:
- SATM: sum_i where N(t) is 0 or 1 depending if
particle i is in a given SHELL at time t. SATM can be used to
calculate the mean residence time of a solvent molecule in a shell
- MRTI: a different definition for the mean residence time where
a simple histogram of the number of consecutive steps a solvent
molecule is in a SHELL is recorded. Thus every time a molecule leaves
a SHELL, all previous data is "forgotten".
- SATX: similar to SATM but gives the cross correlation of two SHELLS
- WREO: water reorientation. average reorientation of single water
molecule dipole moments.
- DDIP: dipole-dipole correlation of given atoms with solvent (TIP3)
- SDDP: same as DDIP but only with waters in a given shell
- VACF: velocity auto correlation function (needs VELO trajectory)
Note: This introduces new ##-keyword 'CORSOL' which selects inclusion of CORSOL
and a secondary keyword 'CORSOLDBL' which toggles single/double precision for
the temporary data during data acquisition (keyword present = REAL*8)
These keywords should not be added to the default pref.dat since this module
is still being enhanced. The currently submitted functionality is working and
stable, but addition of new functionality may lead to changes in the interface.
Files Added:
source/correl/corsol.src
source/correl/ancsol.src
Files Modified:
source/charmm/charmm_main.src
Modified Documentation:
doc/corsol.doc
New Testcases:
test/c34test/corsol_ddip.inp
test/c34test/corsol_wreo.inp
test/c34test/corsol_vacf.inp
test/c34test/corsol_satm.inp
test/c34test/corsol_satx.inp
test/c34test/corsol_mrti.inp
..............................................................................
1.5.2 Prototype Solvent Facility
Certain RDFSOL functionality can at present only be used with TIP3 water
(especially all functions involving dipole moment can only use the moment of
the whole selection). The PROTotype facility extends this functionality to
other solvent molecules and to the analysis of mixtures. PROTotype "sets"
offer a generic way of handling multiply occurring identical subunits in a
given system (e.g all methanol molecules in a water-methanol mixture).
This project provides the basic PROTo functionality and two new CORREL
time series. The new CORRel time series are
PRDI, the sum of all single set dipole moments
(which differs from the overall dipole moment if the single
sets carry a net charge and the dipole moment needs to be
referenced to the center of mass/geometry)
Note: Almost equivalent functionality can be obtained
with the existing DIPO series, but the internal coding
is quite different and provides a prototype for the
combination of PROTO and CORREL
PRVE, the sum of center-of-mass(or geometry) velocities of all sets
Note that new ##-keyword 'PROTO' is introduced, which should be added
to the default pref.dat as it enhances RDFSol.
Files Added:
source/correl/proto.src
source/fcm/proto.fcm
Files Modified:
source/charmm/charmm_main.src
source/charmm/iniall.src
source/correl/correl.src
source/correl/anacor.src
source/correl/shlsel.src
New Documentation:
doc/proto.doc
New Testcase:
test/c34test/prototest.inp
test/c34test/correl_prdi.inp
..............................................................................
1.5.3 RDFSOL Enhancements
Prototype sets can now be used as setA or setB. For each set the center
of geometry (or mass with keyword MASS) will be calculated and used as the
"position" of this set. Similarly, if a dipole moment is required in the
calculation of a function, each set with its dipole moment will be used in
turn.
All supported functions can be calculayed simultaneouly, which eliminates
the need to reread a given trajectory repeatedly.
Files Modified:
source/correl/rdfsol.src
source/correl/rdfsl2.src
Modified Documentation:
doc/rdfsol.doc
New/Modified Testcase:
test/c31test/rdfsol.inp
test/c31test/rdfsol2.inp
test/c34test/rdfsol3.inp
..............................................................................
1.5.4 PERT Enhancements and Fixes
Better support for turning off interactions between two parts of a
system (e.g., decoupling solute from solvent, ligand from protein)
while maintaining *all* interactions in the two parts of the system
themselves. This is useful for following "chemical" paths, hence the
functionality is labelled CHEMical PERT.
Particularly for Ewald this should be considered experimental, hence
all code is protected by ##IF CHEMPERT which, in my opinion, should not be
compiled in by default.
Preliminary support for the isotropic LJ long-range correction
(the ##IF LRVDW code). Provided "real dummy atoms" are used (rather
than playing tricks with RSCAle or WCAD) energy calculations now
support the LJ long-range correction for energies and virial and
compute a free energy contribution if applicable. Generic support
(including the RSCAle/WCAD tricks) requires an overhaul of the way the
correction is computed in the first place and was, therefore, postponed.
Files Modified:
source/charmm/iniall.src
source/fcm/fast.fcm
source/fcm/pert.fcm
source/image/nbondm.src
source/nbonds/nbexcl.src
source/nbonds/nbonda.src
source/nbonds/nbondg.src
source/pert/epert.src
source/pert/pert.src
New/Modified Documentation:
doc/pert.doc
doc/preflx_list.doc (added CHEMPERT keyword)
New Testcase:
test/c34test/chempert1.inp
test/c34test/chempert2.inp
test/c34test/pert_lrc1.inp
test/c34test/pert_lrc2.inp
..............................................................................
1.5.5 Bugfixes
(1) CMAP fails in combination with PERT, but the problem is CMAP's.
c30test/cmaptest.inp does NOT get run since CMAPSET is not set in iniall.src.
If PERT is active, no CMAP lambda=0 get computed. The real culprit is an error
in image/images.src related to the calculation of NCRTT
Files involved:
source/charmm/iniall.src
source/image/images.src
(2) Several PERT related problems are observed.
- Wrong IMAGE Lennard-Jones energy with FAST ON / FAST GENERIC.
- PERT does not work with the fast BYCBim nonbonded list routine. Ideally,
attempting to do so leads to a segfault. However, the Intel compiler manages
to produce numbers which even appear reasonable, which doesn't prevent them
from being utterly wrong.
- The soft core code (PERT/PSSP) does not handle the combination of group
based cut-off with Ewald. Instead of bombing, incorrect values are reported.
- The WCA/softcore code sets the substition variable SSBPLRCSD. This is fine
for the fact that these variable names get truncated to 8 characters. Thus,
each attempt to set this variable sets a new variable SSBPLRCS (note the
missing D !!!). If one goes crazy and creates a situation where this code
is run fairly often, one exceeds the maximum number of substitution
variables and bombs. Interestingly, c32test/repul.inp does not trigger the
problem, but the testcase should be modified to reflect a correct
8-character substitution variable name.
Files involved:
source/image/upimag.src
source/nbonds/nbonds.src
source/pert/pert.src
source/pert/epert.src
test/c32test/repul.inp
(3) FAST GENERIC to correct (V)ATOM VFSWIT EWALD energies. Upon setting FAST
GENERIC (old fast routines), the nonbonded option combination VFSWIT EWALD
is not handled correctly and leads to wrong energies (and forces, presumably).
In the old fast scheme (FAST GENERIC), REWALD was expected to handle
all ATOM / Ewald based functionality. However, it does not support
VFSWit. So far, so good. When REWALD "fails" (cannot accomplish its
task), EVDW should take over. Because of a faulty IF statement,
however, ENBFS8 (which has no clue about EWALD) takes over, leading to
an interesting mix of electrostatic energy terms.
Files involved:
source/nbonds/enbond.src
------------------------------------------------------------------------------
1.6 Multiconformational Charge Fitting with Lone-Pairs
Developers : Victor Anisimov and Alex D. MacKerell
Email Address : victor@outerbanks.umaryland.edu
alex@outerbanks.umaryland.edu
Institution : University of Maryland, School of Pharmacy
Date : June 30, 2006
Previous version of fitcharge did not support multiconformational charge
fitting in presence of Lone pairs. This is fixed in the current version
along with various small bugs. An extended output of CHARMM MESP and its
difference from QM MESP is added for the "TEST" mode of FITCHARGE.
Files Modified:
source/misc/fitcharge.src
doc/fitcharge.doc
------------------------------------------------------------------------------
1.7 Linearly Time-Varing Force
Developer : Bruce Tidor
Email Address : tidor@mit.edu
Institution : Massachusetts Institute of Technology
Date : June 20, 2006
We introduced the possibility of applying a linearly time-varying force,
over the course of a molecular dynamics trajectory. We modified the existing
constant force pulling module to allow for linearly time-varying forces,
by invocation of a reserved keyword (SWITch). A constant force is applied by
default if this keyword is not invoked.
The user can specify the starting and end force amplitudes. The magnitude
of the force is linearly scaled over the course of a molecular dynamics
simulation (through the dynamics command, with leap-frog integrator).
An error message is issued if this command is called during other energy
evaluations.
The current implementation could be adapted to include other types of
functions for the time dependence of the applied force.
Files Modified:
source/energy/epull.src
source/fcm/pull.fcm
Modified Documentation:
doc/cons.doc
New Testcase:
test/c34test/pull_switch.inp
test/data/1ow6.crd
test/data/1ow6_gbsw.rst
test/data/1ow6.psf
------------------------------------------------------------------------------
1.8 TREK Support Files
Name : Fabian Ille, Frank Noe, Stefan Fischer
Email Address : stefan.fischer@iwr.uni-heidelberg.de
Institution : University of Heidelberg, Germany
Date : June-29, 2006
A method for generating an initial path when setting-up a CPR refinement
of a large conformational transition in a protein is described in detail in
Proteins 59, p.534-544, 2005.
The initial path (i.e., a series of transition intermediates) that is to
be refined by CPR is generated by interpolation between the Internal
Coordinates (IC) of the reactant and product end-states
(rather than the default interpolation in Cartesian coordinates).
Interpolation in IC describes well the torsional transitions
between rotameric states of the sidechains. However, when IC-interpolation is
applied to the backbone-torsion angles, it can lead to severe disruption of
the backbone fold. In contrast, Cartesian interpolation approximately preserves
the backbone fold in most cases (if the protein remains compact during the
transition), but often leads to extreme deformation of the sidechains.
Therefore, the two interpolation methods are combined here:
First, the backbone atoms are interpolated in Cartesian coordinates
so as to preserve the backbone fold, and then the sidechain atoms are
built onto the interpolated backbone, using IC that are interpolated between
the values of the end-states.
The initial path build by this "combined interpolation" can be further
improved, so as to avoid unrealistic events such as bond-crossing
or ring-penetration. These can be effectively avoided by shrinking all
the sidechains in each intermediate point of the initial path.
This is achieved by reducing all bond lengths of the sidechains
(for ex. to half the original size) before building them onto the backbone.
At first glance, this approach would seem to be unphysical and
would result in energetically unfavorable paths. However, the minimization
process applied to the path-points during the CPR procedure rapidly
restores the shrunken sidechains to their normal size, while undesirable
events no longer occur in the resulting path.
Files Added:
support/trek/initial_path/00readme
support/trek/initial_path/comb_interpol.inp
support/trek/initial_path/make_traj.str
support/trek/initial_path/mini_interpol.str
support/trek/initial_path/user_def.str
support/trek/initial_path/vector.pl
support/trek/initial_path/frames/interpol_comb_4_steps.dcd
support/trek/initial_path/frames/interpol_comb_4_steps.dcd.pdb
Note that initial_path is put into support/trek/initial_path.tar.gz.
Modified Documentation:
doc/trek.doc
------------------------------------------------------------------------------
1.9 Ensemble Code Enhancements
Developer : Robert Best
Email Address : R.B.Best.00@cantab.net
Institution : National Institutes of Health, USA
Date : July 5, 2006
The ensemble code has been updated to also do hamiltonian exchange
(i.e. replica exchange between different force-fields) and a simple test
case and documentation have been added for this.
A bug in the startup code has been fixed, allowing arguments to be
passed to ensemble jobs launched with MPI. A minor bug in the hqbm_rc8_ens.inp
test case has also been fixed.
Files Modified:
source/machdep/startup.src
source/machdep/ensemble.src
source/fcm/ensemble.fcm
Modified Documentation:
doc/ensemble.doc
New Testcase:
test/c34test/hexrex_ens.inp
test/data/hexrex_parm.inp
Modified testcase:
test/c33test/hqbm_rc8_ens.inp
------------------------------------------------------------------------------
1.10 Developments at NIC-Slovenia
Names : Milan Hodoscek
Email Address : milan@cmm.ki.si
Institutions : National Institutes of Chemistry, Ljubljana, Slovenia
and National Institute of Health, Bethesda, MD, USA
Date : June 30, 2006
1.10.1 REPDSTR: Distributed replica development
Support for parallel REPLICA methods in CHARMM is further
developed to support more functionality as in previous
version. Replica path (RPATH) is fully functional.
New files:
test/c34test/rexc.inp
Files Modified:
doc/repdstr.doc
source/energy/epath.src
source/energy/printe.src
source/fcm/repdstr.fcm
source/gener/repdstr.src
source/machdep/paral3.src
doc/parallel.doc
.............................................................................
1.10.2 Support of ewald for ab initio QM/MM
Giali Gao's method to include ewald functionality into QM/MM
was extended to be used with ab initio QM programs interfaced with the
CHARMM. This includes GAMESS, QCHEM and GAMESSUK ab initio programs.
Files Modified:
source/fcm/mndo97.fcm
source/gukint/gukini.src
source/mndint/mndewald.src
source/nbonds/nbonds.src
source/nbonds/ewaldf.src
source/nbonds/pme.src
source/fcm/gamess.fcm
install.com
doc/mndo97.doc
doc/diesel.doc
.............................................................................
1.10.3 Support for new special purpose molecular dynamics hardware
The new generation MDGRAPE-3 board is now available for general
use and CHARMM was extended to be used with it. Also the support for
older version was ovarhouled, so the code is cleaner to ease further
development.
Files Modified:
source/fcm/grape.fcm
source/nbonds/grape.src
source/nbonds/nbutil.src
doc/nbonds.doc
.............................................................................
1.10.4 Further support for 64 bit machines
Some fixes necessary to support 64 bit machines. Mostly
regarding parallel ab initio QM/MM methods and some other too.
Files Modified:
source/gamint/ddi.src
source/parallel/paral1.src
source/parallel/paral2.src
source/parallel/paral3.src
.............................................................................
1.10.5 pref.dat fixes
Some fixes for ##IF statement
Files Modified:
source/energy/afm.src (missing label)
source/fcm/mndgho.fcm (file was empty ???)
source/mndint/mndene.src (GHO and other fixes)
source/mndint/mndgho.src (GHO fix)
source/mndint/mndini.src (GHO fix)
source/quantum/qmevdw.src (Intel fortran doesn't like empty source files)
source/util/string.src (MMFF, CFF fix)
source/energy/energy.src (for aesthetic reasons)
source/pert/epert.src (for aesthetic reasons)
source/nbonds/nbexcl.src (LRVDW dependency problem)
source/nbonds/nbutil.src (LRVDW,PBEQ dependency problem)
.............................................................................
1.10.6 Other bug fixes
(1) SQUANTUM was not available in the main charmm program
Files Modified:
source/charmm/charmm_main.src
(2) Replacing 0.0 or 0.0d0 with the ZERO from number.fcm
Files Modified:
source/energy/ecnstr.src
source/util/vector.src
(3) cstuff.c support for glibc-2.4
Files Modified:
source/machdep/cstuff.c
(4) New gcc support fixes (gfortran)
Files Modified:
source/machdep/startup.src
(5) Subroutine POWELL name clash with GAMESS
Files Modified:
source/minmiz/minmiz.src
source/minmiz/powell.src
(6) CMAP parameters files don't work with MEDIUM CHARMM
Files Modified:
source/fcm/dimens.fcm
(7) Parallel fix for EEF1
Files Modified:
source/misc/eef1.src
test/c27test/testeef1.inp
1.10.7 All occurrences of mpi/mpif.h changed to mpif.h
All the occurences of the include 'mpi/mpif.h' statements were
simplified and generalized for all the platforms. From now on use just
include 'mpif.h', since install.com and Makefile_ take care of
the problem.
Files Modified:
install.com
source/dynamc/dynamc.src
source/energy/energy.src
source/machdep/machutil.src
source/machdep/paral1.src
source/machdep/paral2.src
source/machdep/paral3.src
source/machdep/startup.src
source/manip/shake.src
source/nbonds/nbndcc.src
source/nbonds/pblist.src
source/nbonds/pmeutil.src
source/quantum/mpiqub.src
source/quantum/qmene.src
source/quantum/qmjunc.src
source/quantum/qubene.src
source/vibran/vibran.src
------------------------------------------------------------------------------
1.11 Developments at the National Institute of Health
Developers : Jhih-Wei Chu, H. Lee Woodcock, Xiongwu Wu,
Paul Sherwood, Milan Hodoscek, George Stan
and Bernard R. Brooks
Email Address : chu@hec.utah.edu, hlwood@nih.gov, wuxw@nhlbi.nih.gov,
p.sherwood@dl.ac.uk, milan@cmm.ki.si,
gstan@helix.nih.gov, brb@nih.gov
Institution : Laboratory of Computational Biology, NHLBI, NIH
Date : July 1, 2006
1.11.1 EMAP bugfix and document update
Bug fix in coorelation fucntion calculation and update in io.doc and
emap.doc about direct read segment id from PDB files.
Files involved:
source/emap/emapsubs.src
doc/io.doc
doc/emap.doc
..............................................................................
1.11.2 NEB abnr minimization code clean up and fixes
The NEB abnr minimization code is cleaned up, matrix solvers have been
moved to source/util.
File added
source/util/svd.src
Files Modified:
source/minmiz/abner.src
..............................................................................
1.11.3 Support for SCCDFTB Replica Path and Nudged Elastic Band
Files Modified:
source/sccdftbint/sccdftbini.src - Replica Path and NEB routines were added
to this file
source/fcm/gamess.fcm - SCCDFTB was added allowed to access
replica section information
Testcases:
test/c34test/sccdftb_butane_rpath.inp - input file for full QM rpath
test/c34test/sccdftb_butane_rpath_qmmm.inp - input file for QM/MM rpath
test/c34test/sccdftb_butane_neb.inp - input file for full QM NEB
test/c34test/sccdftb_butane_rpath.out - output fule for full QM rpath
test/c34test/sccdftb_butane_rpath_qmmm.out - output file for QM/MM rpath
test/c34test/sccdftb_butane_neb.out - output file for full QM NEB
..............................................................................
1.11.4 Bugfix: QM/MM Nudged Elastic Band with Q-Chem
Files Modified:
source/gukint/gukini.src - Location of setting GTOT was fixed
..............................................................................
1.11.5 Bugfix: QCHEM keyword added the QM/MM section of non-bond files
Files Modified:
source/nbonds/enbaexp.src
source/nbonds/enbfast.src
source/nbonds/enbfs8p.src
source/nbonds/enbonda.src
source/nbonds/enbondg.src
source/nbonds/ewald.src
..............................................................................
1.11.6 Bugfix: Protected debug write statement in Replica Path Code
Files Modified:
source/energy/epath.src
..............................................................................
1.11.7 Bugfix: Fixed install.com bug to allow proper SCCDFTB libraries to be
added to Makefiles. Also make some more changes to
support gfotran as a default compiler (parallel,
too). Make binary compatible trajectories for gfortran
on 64 bit machines.
Files Modified:
install.com
build/UNX/Makefile_gnu
..............................................................................
1.11.8 Generalization of constant velocity code (CVELOCI)
Old constant velocity code was replaced by new generalized
version. The functionality of the old is still available by choosing 2
selections.
Files Added:
test/c34test/cveloci.inp
Files Modified:
dynamc/cveloci.src
fcm/cveloci.fcm
dynamc/dynamc.src
dynamc/dynio.src
charmm/iniall.src
doc/dynamc.doc
..............................................................................
1.11.9 Bugfix: The IGMSEL was not properly used in several
routines. One liner fixes:
Files modified:
source/nbonds/nbaexp.src
source/nbonds/enbfast.src
source/nbonds/enbfs8p.src
source/nbonds/enbonda.src
source/nbonds/enbondg.src
source/nbonds/ewald.src
..............................................................................
1.11.10 Bugfix: Parallel TPS: Added 3 calls to communication routines.
Files modified:
source/dynamc/tps.src
..............................................................................
1.11.11 Bugfix: Typo in .fcm file
Files modified:
source/fcm/consta.fcm
..............................................................................
1.11.12 Bugfix: Improper use of ## keywords for QM/MM
Files modified:
source/fcm/mndo97.fcm
..............................................................................
1.11.13 Bugfix: Unified interface for ab initio QM/MM fixes. Now
supports the same functionality for all 3 programs:
Q-Chem, GAMESS-UK, and GAMESS
New files:
test/c34test/gamessuk_neb.inp
test/c34test/gamessuk_qmmm.inp
test/c34test/gamessuk_rpath.inp
Files modified:
source/gukint/gukini.src
source/manip/scalar.src
..............................................................................
1.11.14 Bugfix: Parallel PME fix for gfortran. Protected by
##GFORTRAN. This fix is general and could replace the
other code. It is much simpler in also more efficient code!
Files modified:
source/nbonds/pmeutils.src
source/machdep/paral3.src
..............................................................................
1.11.15 SCPISM Code Optimized: Runs 30% faster, Uses Less Memory
Developer : Peter Steinbach
Email Address : steinbac@helix.nih.gov
Institution : CMM/DCB/CIT, National Institutes of Health
Date : August 9, 2006
The implementation of the SCP continuum solvent model was simplified,
optimized, and tested. It now runs 30% faster and uses memory more
efficiently. A few large two-dimensional arrays are no longer used.
Energies and forces are unchanged, to within roundoff errors.
Files Modified:
source/fcm/scpism.fcm
source/misc/scpism.src
------------------------------------------------------------------------------
1.12 University of Minnesota Developments
Developers : Dan Thomas Major (M), Kwangho Nam (N), and Jiali Gao (G)
Email Address : major@chem.umn.edu,nam@chem.umn.edu,gao@chem.umn.edu
Institution : University of Minnesota
Date : June 30, 2006
1.12.1 Path-Integral with QM/MM potentials
A path-integral (PI) method to account for nuclear quantum corrections
to a classical PMF trajectory. The implementation is based on a double
averaging scheme proposed by Sprik et al. and by Warshel and coworkers
(Sprik, M.; Klein, M. L.; Chandler, D. Phys. ReV. B: Condens. Matter
Mater. Phys. 1985, 31, 4234-4244. and Hwang, J.-K.; Chu, Z.T.; Yadav, A.;
Warshel, A. J. Phys. Chem. 1991, 95, 8445). The PI bisection sampling scheme
is that described in Pollock, E.L.; Ceperley, D.M. Phys. Rev. B 1984, 30, 2555.
The CHARMM implementation has been described in the following papers:
(a) Major, D.T.; Gao, J. Implementation of the bisection sampling method in
path-integral simulations. J. Mol. Graphics Modell. 2005, 24, 121-127.
(b) Major, D.T.; Garcia-Viloca, M.; Gao, J. Path-integral simulations of
proton transfer reactions in aqueous solution using combined QM/MM
potentials. J. Chem. Theory Comput. 2006, 2, 236-245.
The path-integral code was seperated out from the QUANTUM module to
allow it to work with other quantum modules. Additionally, the code was
extensively modified. Within the QUANTUM MODULE, significant speed-up was
achieved by saving all QM/MM 1-electron integrals as well as all 2-electron
QM integrals.
Files Modified:
install.com
doc/qub.doc
source/fcm/qubpi.fcm
source/charmm/charmm_main.src
source/misc/testch.src
source/quantum/mpiqub.src (moved to source/qub)
source/quantum/qmene.src
source/quantum/qub.src (moved to source/qub)
source/quantum/qubene.src (moved to source/qub)
source/squantm/sqnt_qm2_ewald.src90
source/squantm/sqnt_qmmm_int.src90
source/squantm/sqnt_qmmm_util.src90
New Testcase:
test/cquantumtest/qmpathint1.inp
test/cquantumtest/qmpathint2.inp
The following are introduced and modified during the development period
of August 15, 2006 through February 15, 2007. The developments are
based on CHARMM version c34a1. Some enhancements and fixes to c33b1
are also incorporated into c33b2 as described in the c33b2 release note
(ChangeLog.c33).
2.1 TSRI Developments
Developers : Mike Crowley and Charles L. Brooks, III
Email Address : crowley@sripps.edu, brooks@scripps.edu
Institution : The Scripps Research Institute
Date : January 1, 2007
2.1.1 Eliminate non F95/F03 compliant code and obscolescent code
- Remove all FORTRAN90 keword preprocessing keeping only the FORTRAN90 code
- Replace all remaining computed and assigned goto's
- Introduce charmm kinds for specifications of real, integer, and logical
variables
- Some format specifiers fixed (a and x descriptors need a size for output)
Files Added:
source/fcm/chm_kinds.fcm
Files Modified:
install.com fortran90 removed, everything is f90 now
build/UNX/energy.mk
build/UNX/nbonds.mk
source/charmm/charmm_main.src
source/charmm/iniall.src
source/correl/correl.src
source/correl/corsol.src
source/dimb/eispack.src
source/dimb/nmdimb.src
source/dynamc/mts.src
source/dynamc/tamd.src
source/energy/epath.src
source/energy/hqbm.src
source/fcm/rtf.fcm
source/gener/genpsf.src
source/gener/psfsum.src
source/machdep/machio.src
source/manip/fsshake.src
source/nbonds/enbond.src
source/nbonds/ewald.src
source/nbonds/nbndcc.src
source/nbonds/nbutil.src
source/rxncor/adiab.src
source/rxncor/travel2.src
source/rxncor/travel.src
source/util/imsl.src
source/util/selcta.src
source/util/string.src
source/vibran/vibran.src
source/vibran/vibutil.src
..............................................................................
2.1.2 Module conversion for cheq facility
Module conversion of cheq source and fcm files
Prefx Keys:
CHEQ
Files Added:
source/nbonds/cheqmodule.src
Files Removed:
source/fcm/cheqdyn.fcm
Files Modified:
build/UNX/charmm.mk
build/UNX/cheq.mk
build/UNX/correl.mk
build/UNX/dynamc.mk
build/UNX/energy.mk
build/UNX/gener.mk
build/UNX/image.mk
build/UNX/io.mk
build/UNX/manip.mk
build/UNX/mc.mk
build/UNX/minmiz.mk
build/UNX/misc.mk
build/UNX/nbonds.mk
build/UNX/rxncor.mk
build/UNX/util.mk
source/charmm/charmm_main.src
source/charmm/iniall.src
source/correl/anacor.src
source/correl/solana.src
source/dynamc/dcntrl.src
source/dynamc/dynamc.src
source/dynamc/dynamcv.src
source/dynamc/dynamvv.src
source/dynamc/dynio.src
source/dynamc/dynsub.src
source/dynamc/nose.src
source/dynamc/tamd.src
source/dynamc/trnphi.src
source/energy/energy.src
source/energy/eutil.src
source/energy/printe.src
source/gener/genpsf.src
source/gener/modpsf.src
source/image/upimag.src
source/io/coorio.src
source/io/mainio.src
source/io/psfres.src
source/io/rtfio.src
source/io/trajio.src
source/manip/corman2.src
source/manip/corman3.src
source/manip/dynanal.src
source/manip/intcor.src
source/manip/scalar.src
source/mc/mcio.src
source/mc/mvhmc.src
source/minmiz/abner.src
source/minmiz/conjug.src
source/minmiz/egrad1.src
source/minmiz/minmiz.src
source/minmiz/steepd.src
source/misc/distrib.src
source/nbonds/enbfast.src
source/nbonds/enbfs8p.src
source/nbonds/enbonda.src
source/nbonds/enbond.src
source/nbonds/etable.src
source/nbonds/ewaldf.src
source/nbonds/ewald.src
source/nbonds/pme.src
source/pert/block.src
source/pert/icfcnf.src
source/pert/puic.src
source/rxncor/adiab.src
source/rxncor/lupopt.src
source/util/selcta.src
..............................................................................
2.1.3 Module conversion for GB facilities
- Module conversion of genborn, gbmv,gbsw source and fcm files.
- Gb_common module for arrays, parameters, variables shared between all methods
- Other modules: gbsw, gbmv, genborn contain routines and variables specific
to the method.
Prefx Keys:
GENBORN, GBSW, GBMV
Files Added:
source/energy/gb_common.src
Files Removed:
source/energy/gbmv.src
source/fcm/gbmv.fcm
source/fcm/gbsw.fcm
source/fcm/genborn.fcm
Files Modified:
build/UNX/charmm.mk
build/UNX/energy.mk
build/UNX/manip.mk
build/UNX/pert.mk
build/UNX/util.mk
source/charmm/charmm_main.src
source/charmm/iniall.src
source/energy/energy.src
source/energy/gbim.src
source/energy/gbmvmodule.src
source/energy/gbsw.src
source/energy/genborn.src
source/energy/intere.src
source/energy/phmd.src
source/fcm/gbim.fcm
source/manip/scalar.src
source/pert/block.src
source/util/selcta.src
..............................................................................
2.1.4 Module started for nonbond common blocks
Module started for common blocks associated with nonbond routines.
Necessitated by introduction of other modules in which the HEAP data type of
the actual argument cannot match the dummy argument type inside the module:
CCNBA, CCNBB, CCNBC, CCNBD. These are now allocated and deallocated with
fortran allocation of allocatable arrays.
New File:
source/nbonds/nbmodule.src
Files Modified:
build/UNX/energy.mk
build/UNX/image.mk
build/UNX/io.mk
build/UNX/misc.mk
build/UNX/nbonds.mk
source/energy/ediff.src
source/energy/energy.src
source/fcm/fast.fcm
source/image/eimage.src
source/misc/genetic.src
source/nbonds/enbaexp.src
source/nbonds/enbond.src
source/nbonds/ewwnb.src
..............................................................................
2.1.5 Module conversion for new_timer facility
Module conversion of new_timer source and fcm files
Prefx Keys:
NEW_TIMER
Files Removed:
source/fcm/new_time.fcm
Files Modified:
build/UNX/charmm.mk
build/UNX/correl.mk
build/UNX/dynamc.mk
build/UNX/energy.mk
build/UNX/image.mk
build/UNX/manip.mk
build/UNX/mc.mk
build/UNX/nbonds.mk
source/charmm/charmm_main.src
source/charmm/iniall.src
source/correl/rdfsl2.src
source/correl/shell.src
source/dynamc/dcntrl.src
source/dynamc/dynamc.src
source/dynamc/tamd.src
source/energy/energy.src
source/energy/eutil.src
source/image/nbndgcm.src
source/manip/fsshake.src
source/manip/holonom.src
source/manip/shake.src
source/mc/mvhmc.src
source/nbonds/enbfast.src
source/nbonds/enbond.src
source/nbonds/ewald.src
source/nbonds/heurist.src
source/nbonds/nbexcl.src
source/util/new_timer.src
..............................................................................
2.1.6 Module conversion for no-image periodic boundary list
Module conversion of PBLIST source and fcm files.
Prefx Keys:
PBLIST
Files Modified:
build/UNX/cff.mk
build/UNX/charmm.mk
build/UNX/energy.mk
build/UNX/gener.mk
build/UNX/image.mk
build/UNX/nbonds.mk
source/energy/energy.src
source/nbonds/enbfast.src
..............................................................................
2.1.7 Module conversion for PME facilities
Module conversion of pme and column_fft source and fcm files.
Prefx Keys:
PME COLFFT
Files Added:
source/nbonds/pme_column_fft.src
source/nbonds/pme_column_recip.src
Files Removed:
source/fcm/pme.fcm
source/fcm/pme_par.fcm
Files Modified:
bbuild/UNX/charmm.mk
build/UNX/dynamc.mk
build/UNX/energy.mk
build/UNX/nbonds.mk
source/charmm/iniall.src
source/dynamc/dcntrl.src
source/misc/olap.src
source/nbonds/ewaldf.src
source/nbonds/nbndcc.src
source/nbonds/nbutil.src
source/nbonds/pme.src
source/nbonds/pmeutil.src
..............................................................................
2.1.8 Code and preprocessor text removed from all source files
All fortran and c code as well as associated preprocessor text have been
removed for the following architecture preprocessor keywords:
ALLIANT
ARDENT
CM5
CONVEX
CRAY UNICOS T3D
CSPP CSPPMPI
DEC
DELTA
GWS
HAL
IBM IBMRS IBMSP IBMSP1 IBMVM IBMMVS AIX370
INTEL
MACINTOSH
OS2
PARAGON
POSIX
TERRA
ULTRA
VAX
Files Modified:
source/adumb/umb.src
source/charmm/charmm_main.src
source/charmm/iniall.src
source/charmm/miscom.src
source/dynamc/dynio.src
source/dynamc/tamd.src
source/fcm/dimens.fcm
source/fcm/heap.fcm
source/fcm/impnon.fcm
source/fcm/number.fcm
source/graphics/apograph.src
source/graphics/graphx.src
source/machdep/machio.src
source/machdep/machutil.src
source/machdep/paral1.src
source/machdep/paral2.src
source/machdep/paral3.src
source/machdep/parset.src
source/machdep/space.src
source/machdep/startup.src
source/misc/nmr.src
source/misc/ssbp.src
source/nbonds/ace.src
source/quantum/qmset.src
source/util/string.src
..............................................................................
2.1.9 Minor code changes, makefile enhancements, and bugfixes
- Makefiles updated for current compilers and enabling debug install.com flag
- double selection added to "test second"
- PARCMD keyword added for the parcmd code which is only valid for
a small subset of compilers
- Output is protected for all output to outu with (prnlev > 2)
- 64 bit mpi fix for ia64 in shake.srd
- parallel fix in wham.src
- copying strings fixed for only strings with len > 0 in datstr.src
Files Modified:
install.com
doc/test.doc
build/UNX/Makefile_em64t
build/UNX/Makefile_gnu
build/UNX/Makefile_osx
source/charmm/charmm_main.src
source/correl/clustr.src
source/energy/rmsd.src
source/gener/replica.src
source/gukint/gukini.src
source/machdep/cstuff.c
source/manip/shake.src
source/misc/olap.src
source/misc/pbeq2.src
source/misc/pbeq.src
source/misc/testch.src
source/nbonds/nbndcc.src
source/nbonds/nbutil.src
source/pert/wham.src
source/util/datstr.src
source/util/util.src
source/vibran/vibcom.src
..............................................................................
2.1.10 Testcase clean-up
Test cases are fixed and modified to make success or failure detection
possible.
- Sanity checks with exits for tests which may not have the code compiled.
- Checks for exiting tests that should not be run in parallel.
- Correct message echoed for tests not run
- Remove langevin dynamics and abnr minimization for tests that do not require
these features so the results are reproducible and testable
- parallel output fixed with prnlev @pnode where pnode is set in
datadir.def
- tests that can run in parallel even though not parallel code included
- old integrator not used unless essential so tests can run in parallel
- Sections defined with appropriate skipping of sections for features not
compiled or not parallel for parallel runs
- Unnecessarily long dynamics, minimization, MC or other iterative proceedures
reduced to manageable but still meaningful lengths
- Some bugfixes
- Example test added c34test/gbsw_example.inp
following the prescription for tests header comments
New/Modified Testcase:
test/c20test/ictest.inp
test/c20test/maatest.inp
test/c23test/nmrtest1.inp
test/c24test/mmfptest3.inp
test/c24test/pert2.inp
test/c25test/cortst25.inp
test/c25test/fastest.inp
test/c26test/block4.inp
test/c26test/luptst.inp
test/c26test/pathint.inp
test/c26test/whamtest.inp
test/c27test/adumb-enum.inp
test/c27test/adumb-phichi.inp
test/c27test/gb_cff95_na-test.inp
test/c27test/gb_cff95_prot-test.inp
test/c27test/gb_cff-data.inp
test/c27test/gb_mmff94_na-test.inp
test/c27test/gb_mmff94_prot-test.inp
test/c27test/gb_mmff94_test.inp
test/c27test/genborn19.inp
test/c27test/lnx_img.inp
test/c27test/tsoft.inp
test/c28test/gb_fep.inp
test/c28test/mcmd_rst2.inp
test/c28test/mcmd_rst2_slow.inp
test/c28test/mcmd_rst.inp
test/c28test/mcmd_rst_slow.inp
test/c29test/ace-adumb.inp
test/c29test/adumbcorr.inp
test/c29test/rmsdyn.inp
test/c30test/cftiangl.inp
test/c30test/cmaptest.inp
test/c30test/cq1ab1gbdyn.inp
test/c30test/cq1fsvwat.inp
test/c30test/entropylj.inp
test/c30test/entropyosc.inp
test/c30test/test_rmsd2.inp
test/c31test/gbsaim.inp
test/c31test/off_path_simulation.inp
test/c31test/pert-mmfp.inp
test/c32test/argc_cbias.inp
test/c32test/argc_grid.inp
test/c32test/argc_rndm.inp
test/c32test/attr.inp
test/c32test/cons_rmsd_zeta.inp
test/c32test/dscfvib.inp
test/c32test/ips_tip216.inp
test/c32test/mpnoe.inp
test/c32test/repul.inp
test/c33test/gbsw_ff05.inp
test/c33test/hdgb.inp
test/c33test/hqbm_single.inp
test/c33test/nmrtest2.inp
test/c33test/phmd.inp
test/c33test/rush.inp
test/c33test/test_rmsd3.inp
test/c34test/chempert1.inp
test/c34test/chempert2.inp
test/c34test/correl_prdi.inp
test/c34test/corsol_ddip.inp
test/c34test/corsol_mrti.inp
test/c34test/corsol_satm.inp
test/c34test/corsol_satx.inp
test/c34test/corsol_vacf.inp
test/c34test/corsol_wreo.inp
test/c34test/gamessuk_neb.inp
test/c34test/gamessuk_qmmm.inp
test/c34test/gamessuk_rpath.inp
test/c34test/gbmv_vdw.inp
test/c34test/gbsw_example.inp
test/c34test/hdgb_corr3.inp
test/c34test/hdgb_corr4.inp
test/c34test/hdgb_corr5.inp
test/c34test/hexrex_ens.inp
test/c34test/pbcubes.inp
test/c34test/pert_gsbp_gcmc.inp
test/c34test/pert_lrc1.inp
test/c34test/proto.inp
test/c34test/pull_switch.inp
test/c34test/rdfsol3.inp
test/c34test/sccdftb_neb.inp
test/c34test/sccdftb_qmmm.inp
test/c34test/sccdftb_rpath.inp
test/c34test/tamd_ala10.inp
test/c34test/wl_test.inp
test/compare.awk
test/datadir.def
test/seddir
test/test.com
..............................................................................
2.1.11 SSNMR
Files Addrd:
soruce/fcm/ssnmr.fcm
soruce/misc/ssnmr.src
Files Modified:
soruce/charmm/charmm_main.src
------------------------------------------------------------------------------
2.2 VMOD facility and MMFP enhancements
Developer : Charles ROBERT and David PERAHIA
Email Address : charles.robert@u-psud.fr david.perihia@u-psud.fr
Institution : French National Center for Scientific Research (CNRS)
Date : 29 Dec 2006
The VMOD facility (David Perahia, Sylvain Frederic, Charles H. Robert
2002-2006) is used to add one or more terms to the potential energy,
each term corresponding to a restraint to a given mrms projection on
a normal mode or other 3N-dimensional vector. An appropriate reference
is Floquet et al. (2006) FEBS Lett. 580, 5130-6.
This facility is compatible with parallel operation.
The command has three forms: initialization, specification of each mode
restraint, and reset (to free the heap).
Fields for reporting MMFP energies were saturated, and developers had
been led to "borrow" relatively unused fields for their own ends.
To remedy this, we have added a new reporting line labelled MMFP2.
Note:
1) LENENT increased from 80 to 90 to accomodate the VMOD restraint energy
2) New "MMFP2" reporting defined in energy/printe.src
Files Added:
source/fcm/vmod.fcm
test/c34test/vmodwat.inp
Files Modified:
doc/mmfp.doc
source/fcm/mmfp.fcm
source/fcm/energy.fcm
source/misc/mmfp.src
source/energy/energy.src
source/energy/printe.src
source/energy/eutil.src
source/dynamc/dynio.src
------------------------------------------------------------------------------
2.3 Developments at University of Chicago (Benoit Roux)
Developers : Edward Harder, Yuqing Deng, Benoit Roux
Email Address : eharder@uchicago.edu, roux@uchicago.edu,
deng@mcs.anl.gov
Institution : University of Chicago, Argonne National Lab
Date : December 21, 2006
2.3.1 Thole parameters
The parameter that controls the strength of the screened Coulomb
interactions between bonded Drude oscillators has been changed from a
constant to a variable that depends on the identity of the bonding pair.
2.3.2 Miscellaneous RMSD and WCA fix
We added an option to suppress output of chosen rmsd restraints in a
dynamics run. WCA is implemented in the generic fast group routine.
Fixed SSBP long range correction when the cut-off is smaller than SSBP RMAX.
Files Added:
source/fcm/thole.fcm
Files Modified:
doc/drude.doc
doc/cons.doc
doc/pert.doc
source/charmm/charmm_main.src
source/gener/drude.src
source/misc/fitcharge.src
source/pert/epert.src
source/fcm/psf.fcm
source/fcm/rmsd.fcm
source/energy/rmsd.src
source/energy/ecnstr.src
source/nbonds/enbfast.src
source/nbonds/enbond.src
------------------------------------------------------------------------------
2.4 University of Chicago Developments
Developers : Yuqing Deng and Aaron R. Dinner
Email Address : deng@mcs.anl.gov, dinner@uchicago.edu
Institution : Argonne National Lab, University of Chicago
Date : December, 11, 2006
Implementation of atom-based image energy calculations when making MC
moves with PERT active. When PERT is activiated, the MC module constructs
two additional symmetric image lists for the reactants and products.
The energies calculated from these image lists are weighted with the coupling
paramter lambda or 1-lambda.
Files Added:
test/c34test/mc_pert_pbc.inp
Files Modified:
doc/mc.doc
source/mc/mc.src
source/mc/mcener.src
source/mc/mcimge.src
source/mc/mvgcmc.src
------------------------------------------------------------------------------
2.5 Lone-pairs and Drude model enhancements
Developers : Victor Anisimov and Alex D. MacKerell
Email Address : victor@outerbanks.umaryland.edu
alex@outerbanks.umaryland.edu
Institution : University of Maryland, School of Pharmacy
Date : December 29, 2006
The implemented changes have the purpose of reducing the amount
of information printed in the output file when lone-pairs or the
classical Drude polarizable force field are invoked.
Print level is increased to 7 in the assignment of velocities
to Drude particles. The printed material is trivial and
does not include any error or warning information.
The print level is increased to 6 and 7 during generation of the
Drude particles. This stops the printing out of redundant information
that is not essential for the user, which would be accessed at the
default print level (5).
The Drude model uses lone-pairs on hydrogen bond acceptors, leading
to warning messages about the presence of 3-membered rings when the
lone-pairs are generated (This occurs only when ficticious LP-atom
bonds are created to preserve original 1,4 electrostatic terms for
the hydrogen bond acceptor centers, which is a part of the present
Drude electrostatic model).
The present modification disables the 3-member ring test if
I-J-K-L set involves a lone-pair. For other atom types the original
WRNDIE(0) action is preserved. The message that corresponding
dihedral angle will not be generated is shifted to level 7 if
lone-pairs are present in the dihedral. Original message will
appear in absence of lone-pairs.
Note: Current implementation of the lone-pair related fixes uses
AMASS(I).GT.0.002 test to recognize lone-pair sites which is
not a very reliable test. Because lone-pairs are actively used
in the Drude model it is necessary for development purposes to
create a globally accessible list saying whether particular
atom is a lone-pair or not.
Files Modified:
source/dynamc/dcntrl.src
source/gener/drude.src
source/gener/genpsf.src
------------------------------------------------------------------------------
2.6 University of Minnesota Developments
Developers : Wangshen Xie and Jiali Gao
Email Address : xie@chem.umn.edu, gao@chem.umn.edu
Institution : University of Minnesota
Date : December 29, 2006
2.6.1 Second order derivative of polarization energy
Subroutines to calculate second order derivative of polarization energy
are added to original pipf code. PIPF can noew be used to do normal mode
analysis using molvib module. Matrix inverse procedure to obtain induced
dipoles are added to be used to calculate second order derivative and
molecular polarizabilities for small molecules.
2.6.2 PIPF bugfix
In the original PIPF code, when induced dipoles are calculated using SCF
iterations during MD simulations the initial induced dipoles are 0. In order
to decrease the number of interations to converge induced dipoles, the initial
dipoles can now be optionally set to be the converged induced dipoles from
last MD step. The bug in calculating polarization force with Thole's damping
function in the presence of image atoms is fixed by correcting scaling factor.
Files Added:
source/pipf/epfinv.src
source/pipf/vpipf.src
test/c34test/pipf_vib.inp
Files Modified:
doc/pipf.doc
source/nbonds/enbond.src
source/dynamc/dcntrl.src
source/pipf/pfdyn.src
source/pipf/epipf.src
source/pipf/epfimg.src
source/pipf/dpfimg.src
source/fcm/pipf.fcm
------------------------------------------------------------------------------
2.7 Ensemble Code Enhancements
Developer : Robert Best
Email Address : R.B.Best.00@cantab.net
Institution : Laboratory of Chemical Physics, NIH/NIDDK
Date : December 31, 2006
2.7.1 Updates and improvements to ENSEMBLE module
The facility for replica exchange between different force-fields
has been improved. A bug in the test case c34test/hexrex_ens.inp
has been fixed.
2D replica exchange has been added (test case c34test/rex2_ens.inp).
Exponential averaging of multiple energy functions (e.g. as used in
multi-Go approaches) has been added, with a test case c34test/multi_ens.inp.
Prefx Keys: ENSEMBLE
Files Added:
test/data/twop_parm.inp
test/data/swap_rules.dat
test/c34test/multi_ens.inp
test/c34test/rex2_ens.inp
Files Modified:
doc/ensemble.doc
source/energy/energy.src
source/machdep/ensemble.src
source/fcm/ensemble.fcm
test/c34test/hexrex_ens.inp
..............................................................................
2.7.2 Multiple version install.com for each architecture
(1) install.com has been modified so that it can work either in the standard
way, or as below:
./install.com arch.build_name size ...
e.g.
./install.com gnu.large_newrng_ifort large IFORT RNG
./install.com gnu.xxlarge_gfort xxlarge GFORTRAN
(2) A new stopmark, 3, has been added. If this is specified, e.g.
./install.com gnu.large_newrng_ifort large IFORT RNG 3
then install.com sets up the Makefile so building can be done
by simply typing make in the build/gnu.large_newrng_ifort directory
Files Modified:
install.com
..............................................................................
2.7.3 Bugfixes
(1) G95 gives compilation error compiling correl.src
The G95 compiler gives an error relating to the use of a floating
point variable (SERVL) as an index to the array QPRTO on lines
576 and 595 of source/correl/correl.src. The bugfix I give involves
an explicit cast to an integer, though I believe using an
INTEGER variable in the first place would be better.
(2) Offset error when copying time series
When copying a time series B to A, there is an offset of -1 in the
copied series A, and the last value of A is junk. Fixed by initializing
IF1 to zero in subroutine mantim (mantim.src).
(3) Preprocessor error
Change mis-spelled "ENSEMBEL" to "ENSEMBLE" in dynamc/dynio.src
Files involved:
source/correl/correl.src
source/correl/mantim.src
source/dynamc/dynio.src
------------------------------------------------------------------------------
2.8 Karolinska Institute Fixes and Enhancements
Developer : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska Institute
Date : December 31, 2006
(1) Preprocessing keys fixed
Added ##GBMV protection, missing ##ENDIF (scpism_main), ##MPI protection
to quantum/qub.src, and missing ##IF LDM SPACDEC RXNCOR (ldm_routines)
to util/util.src.
Files modified:
source/charmm/charmm_main.src
source/energy/gbmvmodule.src
source/misc/scpism.src
source/quantum/qub.src
source/util/util.src
(2) Correlation bug fix
Fixed the calculation of correlation times for water rotational diffusion.
Does not affect calculations using P1 or P2 keywords.
Files modified:
source/correl/solana.src
(3) OPEN statement fix
Fixed incorrect keyword use in fortran OPEN statement.
Files modified:
source/machdep/paral1.src
(4) Size enhancement
Changed MAXPAD definition to =SIZE for HUGE version
Files modfied:
source/fcm/dimens.fcm
(5) Tolerance change
Some default tolerances changed for SINGLE precision.
SHKTOL 1.0e-5, non-integer charge tolerance=MAX(0.001, 0.001*QTOT)
Files modified:
source/charmm/iniall.src
source/gener/psfsum.src
(6) Bomb level adjustment
"Disallow" bomlev -3 and lower by making this a -1 warning;
Must set bomlev -2 before going lower. Could be applied already at
the -2 level if the VIBRAN -2 warning about large systems is removed.
Files modified:
source/charmm/miscom.src
(7) Compiler option updated
Compiler options modified for gfortran
Files modified:
build/UNX/Makefile_gnu
Note:
- install.com should NOT assume that icc is present just because ifort is
used. gcc works fine.
- install.com should have a "clean" option to set things up for a
re-installation
------------------------------------------------------------------------------
2.9 Zero-order minimization method
Name : Robert Petrella
Email Address : petrella@tammy.harvard.edu
Institution : Harvard University
Date : January 4, 2007
The Zero Module is a general facility for carrying out conformational
searches based on rigid-geometry mapping or so-called "zero-order"
minimization. It also now includes 1st-order minimization methods (Steepest
Descent and Conjugant Gradient), but the fundamental structure of the method
is nonetheless grid-based.
Files Added:
doc/zerom.doc
source/fcm/zerom.fcm
source/zerom/zerom1.src
source/zerom/zerom2.src
Files Modified:
install.com
doc/commands.doc
source/charmm/charmm_main.src
source/charmm/iniall.src
source/fcm/actclus.fcm
source/manip/intcor2.src
source/manip/intcor.src
source/nbonds/nbutil.src
------------------------------------------------------------------------------
2.10 Developments at NIC-Slovenia
Names : Milan Hodoscek
Email Address : milan@cmm.ki.si
Institutions : National Institutes of Chemistry, Ljubljana, Slovenia
and National Institute of Health, Bethesda, MD, USA
Date : December 30, 2006
2.10.1 GAMESS/CHARMM QM/MM interface: support for the latest GAMESS
Support for latest version of GAMESS (7 Sep 2006 R4) released on
December 15, 2006 was added to CHARMM. New development in this version
includes: parallel CC methods, Nuclear-Electron Orbital (NEO). Also
version 3 of DDI communication library is supported.
Files Modified:
doc/gamess.doc
source/gukint/gukini.src
source/gamint/ddi.src
source/fcm/gamess.fcm
source/fcm/consta.fcm
install.com
build/UNX/gamess.mk
build/UNX/gmscomp
tool/actvte.f
.............................................................................
1.10.2 pref.dat and other fixes
Some fixes for ##IF statement and other problems:
Files Modified:
source/correl/shlsel.src (fix ##RDFSOL ##CORSOL order)
source/correl/solana.src (wrong variable name used)
source/energy/gbmvmodule.src (natom missing in setgbmvrad() parameter list)
source/machdep/cstuff.c (error message when hostname not available)
source/mc/moveln.src (typo in routine name)
source/misc/scpism.src (missing ##ENDIF at the end)
source/nbonds/grape.src (##FLUCQ problem)
source/util/util.src (almost everyone needs ASSINT routine!)
source/io/psfres.src (NGRPX,NST2X undefined - please check with
original developer)
source/nbonds/enbaexp.src (TFELEC,ENE,ENN,TFVDW undefined - please check with
original developer)
source/quantum/qmleps.src (VC12 undefined - please check with
original developer)
------------------------------------------------------------------------------
2.11 Florida State University Developments
Developers : Hongzhi Li and Wei Yang
Email Address : yang@sb.fsu.edu
Institution : Florida State University, School of Computational Science
Date : December 24, 2006
2.11.1 PERT/BLOCK hybrid
Code has been added to allow PERT module and BLOCK module (lambda-dynamcs
only) to be used in the same dynamcs simulation. PERT/BLOCK hybrid for enhance
sampling and free energy calculation.
The acdemic purpose is to use lambda-dynamcs (in BLOCK) technique as
enhance-sampling method, while PERT technique as free-energy
calculation method. One application of this algorithm is twin-brother
enhance-sampling method, which will be published soon.
File Added:
test/c34test/pert_block.inp
Files Modified:
doc/pert.doc
source/cff/enbfast_cff.src
source/energy/eintern.src
source/energy/enefscal.src
source/fcm/pert.fcm
source/nbonds/enbonda.src
..............................................................................
2.11.2 Softcore in BLOCK
The softcore method has been extended to BLOCK module in CHARMM.
This project is to allow softcore technique to be implemented to BLOCK
utility in CHARMM. Softcore algorithm is one method to solve the
VDW and ELEC overlapping problem that happens in enhance-sampling
methods.
File Added:
source/fcm/sftc.fcm
test/c34test/block_softcore.inp
Files Modified:
doc/block.doc
source/nbonds/enbonda.src
source/nbonds/enbondg.src
source/pert/block.src
source/pert/epert.src
------------------------------------------------------------------------------
2.12 Developments at Lab of Computational Biology, NIH
Names : Edward O'Brien, Tim Miller and Bernard R. Brooks
Email Address : edobrien@helix.nih.gov, btmiller@helix.nih.gov,
brb@nih.gov
Institution : Laboratory of Computational Biology, NHLBI, NIH
Date : December 31, 2006
2.12.1 Variable Lennard-Jones cutoff method (VLJCM) between atoms
The current CHARMM implementation allows only one Lennard-Jones cutoff
distance for all atoms. VLJCM allows the user to apply different length
lennard-jones cutoff's to different atoms in the system. This is useful
when using force-fields which are parameterized for a specific LJ cutoff
distance (e.g. EEF1) and one wants to introduce new types of atoms which
need larger LJ cutoffs. In this situation VLJCM allows the user to keep
the original LJ cutoff for a certain set of atoms in the system, and apply
a different LJ cutoff to different atoms in the system. VLJCM is setup
before dynamics is run.
Files Added:
source/fcm/varcut.fcm
Files Modified:
doc/scalar.doc
source/image/upimag.src
source/manip/scalar.src
source/nbonds/enbfast.src
source/util/selcta.src
Test Case:
test/c34test/vljtest.inp
.............................................................................
2.12.2 Independent scaling of LJ repulsive and attractive terms
Previous implementations of BLOCK only allowed scaling of the
entire Lennard-Jones equation. Here we allow independent scaling of the
attractive (1/r^6) and repulsive (1/r^12) terms in the Lennard-Jones equation
by introducing new keywords in the call to BLOCK.
Files Modified:
doc/block.doc
source/adumb/eadumb.src
source/cheq/fqener.src
source/dynamc/dynamc.src
source/energy/ediff.src
source/misc/genetic.src
source/nbonds/ace.src
source/nbonds/enbaexp.src
source/nbonds/enbfast.src
source/nbonds/enbfs8p.src
source/nbonds/enbond.src
source/pert/block.src
source/fcm/block.fcm
Test Case:
test/c34test/isljtest.inp
.............................................................................
2.12.3 Linear bond angle warning level down
In a coarse-grained simulation I wanted to have cylinder shaped
molecules. To do this I stringed together atoms and set the bond
angle to 180 degrees (that is linear). To avoid the excessive
number of 'linear bond angle' warnings I get in this system
I changed CHARMM to print out the 'linear bond angle'
warning only if the warning level is below 5. I also slightly
modified the angle calculation.
Files Modified:
source/energy/enefscal.src
..............................................................................
2.12.4 Second derivative code for single-distance RESD terms
Added capability to calculate the single-distance terms of the second
derivative matrix for restrained distances. Calculations requiring the
restrained energy contributions to the Hessian can now be performed.
Files Modified:
source/misc/resdist.src
------------------------------------------------------------------------------
2.13 Parameter Updates
Developers : Alex D. MacKerell
Email Address : alex@outerbanks.umaryland.edu
Institution : University of Maryland, School of Pharmacy
Date : January 3, 2007
2.13.1 Updates in c33b2
1) CMAP term for protonated histidine (RESI HSP) was omitted from
the topology files containing proteins. This was corrected in the
c33b1 release.
2) Special parameters for gbsw model added. See gbsw subdirectory
and parmfile.doc for details (TSRI/Brooks group addition).
..............................................................................
2.13.2 Updates in c34a2
1) Ether parameters added. See top_all34_ethers.rtf and
par_all34_ethers.prm
2) Drude toppar format updated and additional residues/parameters
added.
3) rush parameters for protein folding added. See rush subdirectory
and parmfile.doc for details (TSRI/Brooks group addition).
4) tamdfff parameters added for internal coordinate dynamics. See
tamdfff subdirectory and parmfile.doc for details (TSRI/Brooks group
addition).
Files Added:
toppar/top_all34_ethers.rtf
toppar/par_all34_ethers.prm
toppar/drude/00readme
toppar/drude/models_drude_all.inp
toppar/drude/models_drude_all.out
toppar/drude/models_drude_all_dec06d_c34a2.ene
toppar/drude/toppar_drude_master_dec06d_c34a2.str
toppar/drude/toppar_electric_dec06d_c34a2.str
toppar/drude/positive_drude/ions_swm4_positive_test.inp
toppar/drude/positive_drude/ions_swm4_positive_test.out
toppar/drude/positive_drude/swm4_ion.dat
toppar/drude/positive_drude/swm4_positive_test.inp
toppar/drude/positive_drude/swm4_positive_test.out
toppar/drude/positive_drude/toppar_drude_positive_swm4_ions.str
Files Removed:
toopar/drude.tar.gz
Files Modified:
toppar/top_all22_prot_cmap.inp
toppar/top_all27_prot_lipid.rtf
toppar/top_all27_prot_na.rtf
New/Modified Documentation:
doc/parmfile.doc
------------------------------------------------------------------------------
2.14 Bugfixes
1) Image centering with PSF modified.
When PSF is modified, IMAGE structure is cleaned and image centering
is nullified.
Files fixed:
doc/image.doc
source/image/images.src
2) CMAP parallel code
PSND4 call for CTPA array is fixed
File fixed:
source/io/parmio.src
3) Doubly defined subroutine
FLUSH is defined twice. One is removed.
File Fixed:
soruce/machdep/machio.src
4) VELOcity option for trajectory IO
VELOcity can be written with VELOcity option to the TRAJectory
command.
Files Fixed:
doc/dynamc.doc
source/dynamc/dynio.src
5) PRES format fix
MKPRES writing format is fixed for PRES generation.
File Fixed:
source/gener/mkpres.src
6) Parallel code fix
EEF1 returns with broadcasting data
File Fixed:
source/misc/eef1.src
7) Sun64 Port
SUN 64 bit compilation problem fixed
Files Fixed:
install.com
build/UNX/Makefile_sun64
The following are introduced and modified during the development period
of February 15, 2007 through August 15, 2007. The developments are
based on CHARMM version c34a2.
3.1 TSRI Developments
Developers : Mike Crowley, Jana Khandogin, Ilja Khavrutskii,
Charles L. Brooks, III
Email Address : michael_crowley@nrel.gov, janakhan@scripps.edu,
ikhavru@mccammon.ucsd.ed, brooks@scripps.edu
Institution : The Scripps Research Institute
Date : July 5, 2007
3.1.1 Column fft for better parallel performance in PME
Better code for parallel column fft to reduce communications for high
processor counts and increase load balancing.
Prefx Keys: COLFFT
Files Modified:
source/nbonds/nbutil.src
source/nbonds/pme.src
source/nbonds/pme_column_fft.src
source/nbonds/pme_column_recip.src
source/nbonds/pmeutil.src
test/c26test/pme_p21.inp
..............................................................................
3.1.2 Image facility added to the PHMD module
Constant pH molecular dynamics can be now performed for periodic boundary
systems.
Files Added:
test/c35test/phmd_images.inp
test/data/phmd_hsp.in
Files Modified:
doc/phmd.doc
source/energy/energy.src
source/energy/phmd.src
..............................................................................
3.1.3 Harmonic Fourier Beads Method
Harmonic fourier bead method for transition path optimization and
identification.
Files Added:
doc/hfb.doc -->> missing
test/c35test/trek_hfb.inp
Files Modified:
source/rxncor/adiab.src
source/rxncor/travel.src
source/rxncor/travel2.src
..............................................................................
3.1.4 RMSD constraint code changed to module
RMSD code changed to module to aid in revitalizing the second-selection
mode.
Files Modified:
source/dynamc/dcntrl.src
source/energy/ecnstr.src
source/energy/rmsd.src
source/manip/cstran.src
..............................................................................
3.1.5 Various fixes and enhancements
Files Modified:
source/correl/rdfsol.src uninitialized variable fixed
source/dynamc/dynamc.src io control fixed
source/dynamc/dynamvv.src io control fixed
source/energy/gbsw.src deallocation of unallocated array
source/manip/shake.src typo in pref keyword MPI_AIX64 fixed
source/nbonds/enbond.src getmaxnprs() fix for Intel compiler
source/nbonds/ewald.src getmaxnprs() fix for Intel compiler
source/nbonds/pme_column_recip.src cheq module migration error fixed
source/util/parse.src Added ?iseed as query variable
------------------------------------------------------------------------------
3.2 Re-introduction of GBMV Additions into Fortran 90 Module
Developer: : Michael Feig
Email Address : feig@msu.edu
Institution : Michigan State University
Date : June 30, 2007
During the switch of GBMV to Fortran 90, recent additions to the
GBMV module were lost (in particular the VDWaals code). This update
re-introduces previously submitted updates.
Files Modified:
doc/gbmv.doc
source/energy/gbmvmodule.src
------------------------------------------------------------------------------
3.3 University of Chicago Developments
Developers : Edward Harder, Yuqing Deng and Benoit Roux
Email Address : eharder@uchicago.edu, deng@mcs.anl.gov, roux@uchicago.edu
Institution : University of Chicago, Argonne National Lab
Date : July 3, 2007
3.3.1 New Format for Topology/Parameters of Drude Mode
A new format encodes the Drude model from the RTF. In the present
implementation the drude particles are generated for all atoms for which
polarizabilities (ie. via ALPHA) are specified in the RTF file.
This allows for the drudes to be generated automatically when a molecule
is generated in CHARMM. In addition, code has been developed to allow for
inclusion of atom-based Thole scale factors, atom-based anisotropic
polarizabilities and the addition of lone pairs to selected atoms at
the RTF level. These enhancements allow for all the information for the
polarizable drude force field to be included in the RTF and parameter files.
Files Removed:
source/fcm/thole.fcm
Files Modified:
doc/drude.doc
doc/fitcharge.doc
doc/tpcntrl.doc
doc/lonepair.doc
source/charmm/charmm_main.src
source/charmm/iniall.src
source/energy/energy.src
source/fcm/aniso.fcm
source/fcm/dimens.fcm
source/fcm/psf.fcm
source/fcm/rtf.fcm
source/gener/drude.src
source/gener/genpsf.src
source/gener/modpsf.src
source/gener/update.src
source/io/parmio.src
source/io/psfres.src
source/io/rtfio.src
source/manip/corman.src
source/misc/fitcharge.src
source/nbonds/nbexcl.src
source/pert/epert.src
source/util/array.src
..............................................................................
3.3.2 Various updates and enhancements
New GSBP cavity potential for the sphere calculation is introduced.
A WCA repulsive potential is placed before the dialectric boundary to prevent
water molecules going out of the atomistic simulation region.
In the generalized multiple calculation, all the charges are included (even if
they could be outside the atomistic region) to avoid discontinuity in the
electrostatic potential.
Read and write the multipole expansion coefficients and external field
(PHIX) in card format. Fixed a bug when the large box calculation has more
grid points than the focused box in GSBP setup calculation.
Exclude GCMC ghost atoms from the extended electrostatics calculation and
from the single distance restraint potential. Removed the temporary WCAD array
on the stack and passed WCAD from psf in QCGSET and CGINV. Increase the number
of maximum selection definitions to 200 in fcm/selcta.fcm
Files Modified:
doc/pbeq.doc
source/energy/energy.src
source/fcm/selcta.fcm
source/misc/pbeq2.src
source/misc/gsbp.src
source/misc/mmfp.src
source/nbonds/nbondg.src
source/nbonds/exelec.src
source/nbonds/cheqmodule.src
------------------------------------------------------------------------------
3.4 QUB (QM/MM path integral) Updates
Developers : Dan Thomas Major and Jiali Gao
Email Address : majort@mail.biu.ac.il and gao@chem.umn.edu
Institution : Bar-Ilan University, Israel and University of Minnesota
Date : June 30, 2007
3.4.1 Enhancement to QUB module
The code has been significantly updated and now includes three submodules
(QCP,BQCP, and QFEP). QCP performs standard Quantized Classical Path, BQCP
performs QCP with bisection sampling, while QFEP performs mass-perturbation
BQCP. The latter allows for accurate estimates of kinetic isotope effects in
condensed phase reactions (See doc file for some tech. references).
3.4.2 Path-Integral coupling with QM/MM methods
The code is coupled with the QUANTUM, SQUANTM, and SCCDFTB modules.
In particular, the coupling with QUANTUM and SQUANTM is tight, and a number
of efficient enhancements have been implemented.
With QUANTUM and SQUANTM gradient calculations are automatically turned off
for efficiency, and for QUANTUM the 1- and 2-electron integrals for QM atoms
not described as path-integrals are stored by QUB to avoid recalculation
during path-integral sampling. This will be done for SQUANTM in the near
future as well.
3.4.3 Parallel Code
QUB runs in parallel with both QUANTUM and SQUANTM. QUB takes control
of parallel run instead of QUANTUM and SQUANTM, as it scales nearly linearly
with number of processors. QUB doesn't run in parallel with SCCDFTB, yet.
Files Added:
test/cquantumtest/qmpathint1.inp
test/cquantumtest/qmpathint2.inp
test/cquantumtest/sqmpathint1.inp
test/cquantumtest/sqmpathint2.inp
Files Modified:
doc/parallel.doc
doc/qub.doc
source/charmm/charmm_main.src
source/charmm/iniall.src
source/fcm/qubpi.fcm
source/fcm/squantm.fcm
source/quantum/qub.src
source/quantum/mpiqub.src
source/quantum/qubene.src
------------------------------------------------------------------------------
3.5 GHO Method Interfac to SCC-DFTB (GHO-SCCDFTB)
Developers : Jingzhi Pu and Jiali Gao
Email Address : pu@tammy.harvard.edu; gao@chem.umn.edu
Institution : Harvard University
Date : July 1, 2007
The origianl implementation of GHO-SCCDFTB in c34a2 has a restriction
that all GHO boundary atoms have to be placed at the end of the QM
fragment. This limitation is inherited from an earlier GHO implementation
for the semiempirical module QUANTUM in CHARMM (see doc/qmmm.doc,
GLNK: Restrictions; a common practice is to write a new residue for
QM atoms and place GHO boundary atoms at the end of that residue).
This restriction is now removed by rearranging the list of QM atoms
internally in CHARMM. The source files need to be modified are:
A bug has been fixed for GHO-SCCDFTB gradient. This bug caused
wrong gradient if the compiler does not initialize a real type
variable to zero when it is declared (for example, g77 under Linux).
We fixed this bug by initializing some variables explicitly.
Files Added:
test/cquantumtest/buta_ghosccdftb.inp
Files Modified:
source/sccdftbint/sccdftbini.src
source/sccdftbint/stbgho.src
------------------------------------------------------------------------------
3.6 Semiempirical QM/MM SQUANTM and MNDO97 Updates
Developers : Kwangho Nam
Email Address : nam@tammy.harvard.edu
Institution : Harvard University
Date : June 30, 2007
3.6.1 SQUANTM Fortran90 format change
The format of SQUANTM semiempirical QM/MM module is changed to
comply with other CHARMM source format, allowing other CHARMM fcm
files can be used. This change removes a specific preprocessing
step in the compilation, though the module only supports Fortran90
compilers. (Platform tested includes GNU, ALTIX, IBMAIX, and
IBMAIXMP.)
3.6.2 SQUANTM Parallel implementation
The module is parallelized, and a memory management is improved
when using QM/MM-Ewald summation method. The reciprocal K-space
terms require a huge memory allocation, and current modification
breaks down the memory allocation to each processor evenly but does
not require internode communication.
3.6.3 QM/MM Gaussian core-core interaction
To be consistent with other semiempirical QM/MM module in CHARMM,
Gaussian core-core interaction is introduced for AM1 and PM3 methods,
and a keyword is also introduced to turn off this interaction to be
compatible with older versions.
3.6.4 Bug fixes for MNDO97 and SQUANTM compilations.
Several bugs are fixed for a smooth compilation of MNDO97 and
SQUANTM module. In the MNDO97 module, the current fixes will allow
the use of GHO method as a default.
Files Added:
build/UNX/squantm.mk
source/squantm/sqnt_qm2_energy.src
source/squantm/sqnt_qm2_ewald.src
source/squantm/sqnt_qm2_gho.src
source/squantm/sqnt_qm2_grad.src
source/squantm/sqnt_qm2_mopac.src
source/squantm/sqnt_qmmm_int.src
source/squantm/sqnt_qmmm_module.src
source/squantm/sqnt_qmmm_util.src
source/fcm/qm2_array_locations.fcm
source/fcm/qm2_constants.fcm
source/fcm/qm2_conversions.fcm
source/fcm/qm2_double.fcm
source/fcm/qm2_elements.fcm
source/fcm/qm2_parameters.fcm
Files Removed:
build/UNX/squantm.mk_altix
build/UNX/squantm.mk_gnu
build/UNX/squantm.mk_ibmaix
build/UNX/squantm.mk_ibmaix64
source/squantm/sqnt_qm2_energy.src90
source/squantm/sqnt_qm2_ewald.src90
source/squantm/sqnt_qm2_gho.src90
source/squantm/sqnt_qm2_grad.src90
source/squantm/sqnt_qm2_mopac.src90
source/squantm/sqnt_qmmm_int.src90
source/squantm/sqnt_qmmm_module.src90
source/squantm/sqnt_qmmm_util.src90
source/squantm/assert.h
source/squantm/constants.h
source/squantm/conversions.h
source/squantm/dprec.h
source/squantm/qm2_array_locations.h
source/squantm/qm2_elements.h
source/squantm/qm2_parameters.h
Files Modified:
install.com
doc/qmmm.doc
doc/mndo97.doc
source/charmm/iniall.src
source/energy/energy.src
source/fcm/gamess.fcm
source/fcm/mndgho.fcm
source/mndint/mndo97q/gnu.mak
source/squantm/sqnt_ene.src
source/squantm/sqnt_nbnd.src
source/squantm/sqnt_setup.src
------------------------------------------------------------------------------
3.7 Z-Module Updates and Various Enhancements
Developer : Robert J. Petrella
Email Address : petrella@fas.harvard.edu
Institution : Harvard University
Date : June 30, 2007
3.7.1 IRANdom random integer generator
IRANdom command--generates series of random numbers from uniform
distributions.
Files Modified:
doc/miscom.doc
source/charmm/miscom.src
source/util/random.src
..............................................................................
3.7.2 SECOnd comparison coordinate set
SECOnd comparison coordinate set for use in coordinate manipulation
commands
Prefx Keys: COMP2
Files Modified:
doc/corman.doc
source/fcm/coordc.fcm
source/gener/genpsf.src
source/io/mainio.src
source/manip/corman.src
..............................................................................
3.7.3 Z Module Update
ZMODule (structure prediction module) is refined and enhanced:
- compatibility with CMAP and Urey-Bradley terms added
- call to SUBROUTINE CODES implemented
- name changed from ZERO module
- other minor changes
Prefx Keys: ZEROM, ACTBOND
Files Modified:
doc/zerom.doc
source/charmm/charmm_main.src
source/fcm/actclus.fcm
source/zerom/zerom1.src
source/zerom/zerom2.src
..............................................................................
3.7.4 Bonded energy terms for active atoms
Facility for selecting atoms to be included in bonded energy
calculations.
Prefx Keys: ACTBOND
Files Modified:
source/charmm/iniall.src
source/energy/eintern.src
source/energy/enefscal.src
source/energy/energy.src
------------------------------------------------------------------------------
3.8 Reading/Writing NAMD binary file in CHARMM
Developer : Andrei A. Golosov and Milan Hodoscek
Email Address : agolosov@tammy.harvard.edu
Institution : Harvard University
Date : June 30, 2007
CHARMM is now able to read and write NAMD (molecular dynamics program
from Klaus Schulten's lab) binary coordinates/velocities restart
files. To do this, READ_NAMD and WRITE_NAMD subroutines are called in
source/io/mainio.src These routines are written in C in
source/machdep/cstuff.c
Support files have been added for conversion of CHARMM psf file into
NAMD xplor psf file and creation of auxilarily pdb files for NAMD
necessary for simulations of solvated systems with fixed and
harmonically restrained solute.
Files Added:
support/namd/namdpsf.inp
support/namd/fix_solute.inp
support/namd/harm_rest_solute.inp
test/c35test/namdio.inp
Files Modified:
doc/io.doc
source/io/mainio.src
source/machdep/cstuff.c
------------------------------------------------------------------------------
3.9 Karolinska Institute Fixes and Enhancements
Developer : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska Institute
Date : June 28, 2007
3.9.1 Fast nonbonded interactions using lookup tables
Fast (twofold speedup vs ENBAEXP) lookup tables implemented for
solvent-solvent, solvent-solute and solute-solute interactions. All nonbonded
schemes handled by ENBAEXP (including real space part of PME) are handled.
For now only three site water models can be used (TIP3P, SPC, SPC/E), but TIP4P
is being implemented. The code works in parallel and with peridic boundary
conditions. Non-bonded lists generated with BYGRoup or BYCB options work.
The code is protected by pref.dat keyword LOOKUP. Previous keywords (SLVSLV,
LNTAB1) are obsolete and have been removed in the supplied files.
[Note] There is a problem with the testcase when running in parallel on more
than 2 CPUs; part of the testcase uses a very small system and this causes
some list to be empty when the job is split over 4 CPUs. For real systems
there is no problem.
Files Added:
source/nbonds/elookup.src
source/nbonds/lookup_module.src
test/c35test/lookup.inp
Files Removed:
source/nbonds/ewwnb.src
test/c34test/nbsolv.inp
Files Modified:
doc/nbonds.doc
source/charmm/iniall.src
source/charmm/miscom.src
source/energy/energy.src
source/image/eimage.src
source/image/nbndgcm.src
source/image/upimag.src
source/nbonds/nbonds.src
source/nbonds/nbutil.src
source/nbonds/enbaexp.src
source/fcm/dimens.fcm
..............................................................................
3.9.2 Bugfixes
File modified
source/correl/solana.src Missing IREAL4 in call to FREHP
source/dynamc/dynio.src Constant in calls to extractint8, writint4,
source/util/datstr.src fillint4 replaced with variable
source/image/images.src Memory allocation for PBCUBES and IMCUBES fixed
------------------------------------------------------------------------------
3.10 Developments at the National Institute of Health
Developers : H. Lee Woodcock and Bernard R. Brooks
Email Address : hlwood@nih.gov and brb@nih.gov
Institution : Laboratory of Computational Biology, NHLBI, NIH
Date : July 1, 2007
Extensions for QM/MM and Reaction Path Methods are
1. Full QM/MM Normal Mode Analysis via Q-Chem
2. Delocalized Gaussian Blurred MM charges support added via Q-Chem
3. Added Block support to SCC-DFTD replica path/NEB method
4. Clean up of SD minimizer (i.e. removal of unnecessary pathway method code)
5. Fixed NEB SD minimzer to decouple off-path and in-path forces during
minimizations
Prefx Keys: QCHEM, SCCDFTB, REPLICA, RPATH, GAMESS, GAMESS-UK
Files Added:
test/c35test/qm-mm_dgmm.inp
test/c35test/qm-mm_nmodes.inp
test/data/qchem_gpc.inp
test/data/qchem_pc.inp
test/data/qm-hess.inp
test/data/qmmm-hess.inp
Files Modified:
doc/gamess-uk.doc
doc/qchem.doc
doc/replica.doc
doc/sccdftb.doc
source/charmm/iniall.src
source/energy/energy.src
source/fcm/gamess.fcm
source/gukint/gukini.src
source/minmiz/steepd.src
source/sccdftbint/sccdftbini.src
------------------------------------------------------------------------------
3.11 Developments at NIC-Slovenia
Developer : Milan Hodoscek
Email Address : milan@cmm.ki.si
Institutions : National Institutes of Chemistry, Ljubljana, Slovenia
and National Institute of Health, Bethesda, MD, USA
Date : June 30, 2007
3.11.1 GAMESS/CHARMM QM/MM interface: support for the latest GAMESS
Support for the latest version of GAMESS (24 MAR 2007 R1) was
added to CHARMM. New development in this version includes: TD-DFT
method, many new functionals were added totaling to almost 50, another
MP2 parallelization, etc. Also the interface code uses XXLARGE charmm
as default.
Files Modified:
build/UNX/gamess.mk
build/UNX/gmscomp
doc/gamess.doc
doc/diesel.doc
source/fcm/gamess.fcm
source/gamint/ddi.src
source/gukint/gukini.src
tool/actvte.f
.............................................................................
3.11.2 REPDSTR
The REPlica DiSTRibuted functionality was further extended:
parallel IF, STREam, OUTU is also working now.
Files Modified:
doc/repdstr.doc
doc/replica.doc
source/charmm/charmm_main.src
source/charmm/iniall.src
source/charmm/miscom.src
source/energy/energy.src
source/energy/epath.src
source/fcm/repdstr.fcm
source/fcm/stream.fcm
souce/gener/repdstr.src
source/io/mainio.src
source/machdep/paral1.src
source/util/parse.src
source/util/title.src
test/c34test/rexc.inp
.............................................................................
3.11.3 Torsional Cross Term: CMAP
The CMAP code was extended to support REPLICA and BLOCK
Files modified:
source/energy/ecmap.src
source/fcm/block.fcm
source/gener/replica.src
source/gener/update.src
source/pert/block.src
.............................................................................
3.11.4 Small fixes:
Files modified:
source/cff/enbfast_cff.src (##IMCUBES vs. ##PBCUBES)
source/cff/ewald_cff.src (##IMCUBES vs. ##PBCUBES)
source/correl/rdfsol.src (SOLPRT() -> WSOLPRT() conflict with GAMESS)
source/dynamc/dcntrl.src (##LDM added to compile ##PERT without it)
source/energy/energy.src (##BANBA added to ##IF)
source/machdep/cstuf.c (OpenMPI fix)
source/machdep/startup.src (##PARCMD fix)
source/manip/corman.src (write(*,*) fix)
source/misc/mmfp.src (INTEGER(4) vs INTEGER(8) problem)
source/misc/scpism.src (DERVIS() -> SCDERIVS() conflict with GAMESS)
source/misc/pbeq2.src (ADDINT() -> PBADDINT() conflict with GAMESS)
source/nbonds/pblist.src (##FORTRAN90 - deprecated)
test/c33test/hqbm_single.inp (old integrator not parallel!)
test/c34test/vmodwat.inp (vibran and quasi not parallel!)
test/c34test/testzero.inp (if ?zerom was missing)
------------------------------------------------------------------------------
3.12 Block and QM/MM Normal Mode Updates
Developer : Qiang Cui
Email Address : cui@chem.wisc.edu
Institution : University of Wisconsin - Madison
Date : July 2, 2007
3.12.1 Block normal mode, QM/MM normal mode
Compilation problems with the VIBBLOCK flag are fixed. A problem that
QM/MM NMA with REDU FIX FINITE doesn't work for large systems is fixed.
Files Modified:
source/misc/hbuild.src HSBLC to 0 fix for !##VIBBLOCK
source/misc/fitchrg.src Add protection (##IFN VIBBLOCK) for PYTHAG
source/energy/hqbm.src Misspelling VIBBLOCK as VIBBLOVK (2 times)
source/vibran/vibblock.src Remove the definition/references of ATOMON
source/misc/eef1.src
..............................................................................
3.12.2 For QM/MM NMA
In the section that processes 'REDU',somehow some key changes
(the avoid of allocating the hessian for the entire system even when many
atoms are fixed) have been taken out. QC put back in.
Files Modified:
source/vibran/vibran.src
------------------------------------------------------------------------------
3.13 Developments at University of Vienna
Developers : Stefan Boresch
Email Address : stefan@mdy.univie.ac.at
Institution : University of Vienna
Date : May 7, 2007
This fix addresses two distinct problems:
I. Having a lot of nonbonded exclusions in a RESI entry in the RTF (e.g.
useful to simulate dual topology with PERT) can result in a buffer
overflow in SUBROUTINE MAKINB (nbexcl.src). NOTE: The bug was discovered
in connection with PERT, but is completely independent of any PERT use!
II. Switching extended electrostatics on and off while PERT is
activated causes crashes.
Files involved:
source/pert/pert.src
source/nbonds/nbexcl.src
source/nbonds/nbonds.src
source/nbonds/nbutil.src
------------------------------------------------------------------------------
3.14 Bugfixes and Enhancements
3.14.1 ifort v8.0 compilation
Developer : Robert Best
Email Address : r.b.best.00@cantab.net
Institution : NIH
Date : March 9, 2007
CHARMM will not compile with ifort v8.0 due to the variable N used prior
to declaration in pme.src, subroutine CFFTF. Declaration of n is switched to
before declaration of wsave(4*n).
Files involved:
source/nbonds/pme.src
..............................................................................
3.14.2 Parallelization of the SCP-ISM
Developer : Sergio A. Hassan
Email Address : mago@helix.nih.gov
Institution : CMM/DCB National Institutes of Health
Date : June 20, 2007
The SCP-ISM (Screened Coulomb Potentials-Implicit Solvent Model) was
parallelized using standard MPI routines coded into the scpism.src.
Files Modified:
doc/scpism.doc
source/fcm/scpism.fcm
source/misc/scpism.src
..............................................................................
3.14.3 X11 color map
Developer : Rick Venable
Email Address : venabler@nhlbi.nih.gov
Institution : NIH/NHLBI
Date : July 6, 2007
Colors were not displayed properly for the X11 screen graphics.
Declare INTEGER*4 COLOR_MAP instead of INTEGER.
[Note] Promotion of all INTEGER variables to INTEGER*8 led to a word length
mismatch for the COLOR_MAP array, which is passed to a C routine.
Files involved:
source/fcm/graph.fcm
The following are introduced and modified during the development period
of August 15, 2007 through February 15, 2008. The developments are
based on CHARMM version c34b1.
4.1 IPS Improvements
Developer : Xiongwu Wu and Bernard R. Brooks
Email Address : wuxw@nhlbi.nih.gov
Institution : Laboratory of Computational Biology, NHLBI, NIH
Date : December 28, 2007
2D IPS and 1D IPS formula are replaced by a newly developed 2+1D IPS formula
to extend its application ability. VIPS (both 3D and 2+1D IPS) can be combined
with EWALD method in a simulation.
Files involved:
build/UNX/Makefile_sgi
build/UNX/Makefile_sgi64
doc/nbonds.doc
install.com
source/energy/energy.src
source/fcm/nbips.fcm
source/machdep/machutil.src
source/machdep/startup.src
source/nbonds/enbaexp.src
source/nbonds/enbfast.src
source/nbonds/enbips.src
source/nbonds/enbond.src
source/nbonds/enbonda.src
source/nbonds/enbondg.src
source/nbonds/nbutil.src
source/vibran/vibran.src
test/c32test/ips_tip216.inp
------------------------------------------------------------------------------
4.2 Karolinska Institute Fixes and Enhancements
Name : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska institutet
Date : December 28, 2007
(1) Changed an EQUIVALENCE statement that caused F90 compilation problems
Files involved:
source/correl/solana.src
(2) Documented the NAME keyword for READ/WRITE commands
Files involved:
doc/io.doc
(3) Improved energy reporting when using LOOKUP NOENERGY
With the NOENERGY option the LOOKUP code only calculates the energies when
the non-bond list is updated. For image energies intermittently stored energy
was not properly reset, and hence reported energies could show jumps (no effect
on the dynamics though since forces are not affected).
Also added a lookup testcase.
Files involved:
source/image/eimage.src
test/c34test/lookup.inp
------------------------------------------------------------------------------
4.3 Bugfixes
4.3.1 Bug fixed for trace-statistics collection routine in umbrella sampling
Name : Yousung Jung
Email Address : yousung@caltech.edu
Institution : California Institute of Technology
Date : September 11, 2007
CHARMM version: c33b2
In the present code (rxnene.src) of umbrella sampling, one can have more
'hits' in the .stt file than the number of MD steps actually taken, because
of the way the statistics is collected currently using the variable 'rxncnt'.
This would then yiled the free energy that is incorrect. This problem is
described also in rxnene.src.
In the fixed code, I use the actual MD step (MDSTEP2 = ISTEP) as a
control variable for updating the trace-statistics.
Files involved:
source/charmm/iniall.src
source/dynamc/dynamc.src
source/fcm/rxncom.fcm
source/rxncor/rxnene.src
source/rxncor/rxndef.src
..............................................................................
4.3.2 CLK_TCK Definition fixed
Developer : Mikhail Wolfson
Email Address : wolfsonm@mit.edu
Institution : MIT
Date : January 29, 2008
In the file source/machdep/cstuff.c, lines 391 - 393 read:
#if defined(CLOCKS_PER_SEC) /* fix for glibc-2.4 */
#define CLK_TCK CLOCKS_PER_SEC
#endif
This is incorrect. CLK_TCK and CLOCKS_PER_SEC do not have the same value on
many systems. It is fixed to
#if !defined(CLK_TCK) /* fix for glibc-2.4 */
extern long int __sysconf (int);
# define CLK_TCK ((__clock_t) __sysconf (2)) /* 2 is _SC_CLK_TCK */
#endif
Files involved:
source/machdep/cstuf.c
..............................................................................
4.3.3 Calling argument list fix (charmm.org forum)
tmdrhof removed from the calling argument list for shiftz
Files involved:
source/dynamc/dynamc.src
..............................................................................
4.3.4 SCCDFTB bugs fixed
Developers : Qiang Cui
Email Address : cui@chem.wisc.edu
Institution : University of Wisconsin, Madson
Date : October 27, 2007
Free HEAP properly and initialize NSCCRP when SCCDFTB in use.
Files involved:
source/misc/gsbp.src
source/misc/pbeq.src
..............................................................................
4.3.5 MOLVIB document updated
Developer : Kenno Vanommeslaeghe
Email Address : kenno@outerbanks.umaryland.edu
Institution : University of Maryland, Baltimore
Date : January 8, 2008
Ducument the definition of linear bend internal coordinates in MOLVIB.
Files involved:
doc/molvib.doc
