ChangeLog.c36
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About CHARMM36 Development |
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At the July 2008 CHARMM meeting (Harvard University, July 11-12, 2008),
we decided to release CHARMM c35b1 with incorporating enhancements and fixes
to the developmental version c35a2. Some features stiil under testing will
not be included in the release: Dynamic Importance Sampling (DIMS), Generic
Parameter Optimization Module (FITPARAM) and Genetic Neural Network for QSPR
(GNN). The modified source code and features are described in ChangeLog.c35,
[3] c35b1 Change Log.
As an on-going project, CHARMM development will be carried out
with CHARMM version 36a series. The following describes new features
and enhancements incorporated in the c36 development period.
The following are introduced and modified during the development period
of February 15, 2008 through August 15, 2008. The developments are
based on CHARMM version c35a2. Some enhancements and fixes to c35a2
are also incorporated into c35b1 as described in the c35b1 release note
(ChangeLog.c35).
1.1 Harvard University Developments
Developers : Robert Petrella
Email Address : petrella@fas.harvard.edu
Institution : Harvard University
Date : June 25, 2008
1.1.1 Faster Image List Generation (MKIMAT2)
Linear-scaling code to generate the image lists, based partially
on MKIMAT. Invoked on the command line with the IMFAst option of the update
command. IMFAST preprocessor keyword controls compilation.
Prefx Keys: IMFAST
Files Added:
source/ltm/image_ltm.src
Files Modified:
install.com
build/UNX/image.mk
doc/images.doc
source/fcm/actclus.fcm
source/fcm/image.fcm
source/gener/update.src
source/image/upimag.src
source/nbonds/nbutil.src
..............................................................................
1.1.2 Creation of "base module" directory (ltm).
The ltm directory is intended as a repository of fortran modules
containing only global or "long-term-memory" arrays (allocatable or
non-allocatable) and global variables. The modules are not to contain
procedures (functions or subroutines) or variables/arrays that are local
to other modules, and they are not to have any dependencies.
Intent is organizational; to be compiled early.
Files Added:
build/UNX/ltm.mk
Files Modified:
build/UNX/objlibs.mk
------------------------------------------------------------------------------
1.2 MIT Developments
Developer : Victor Ovchinnikov, Bernhardt L. Trout, Martin Karplus
Email Address : ovchinnv@MIT.edu
Institution : Massachusetts Institute of Technology
Date : June 28, 2008
1.2.1 Conformational consistency
Current methods for generating transition paths between macromolecules
e.g., the TMD and TREK modules, rely on the Cartesian coordinates of a subset
of atoms in a protein. Although several residue types possess symmetry
(e.g. planar symmetry of a PHE ring), so that the conformation of such
a residue is invariant with respect to a rotation around the symmetry axis,
rendering certain groups of atoms effectively indistinguishable, topology
files must distinguish between these atoms (e.g. PHE CD1 vs. PHE CD2).
Given two different coordinate sets for a macromolecule, any two-set path
generation method that makes use of the Cartesian coordinates of atoms that
belong to residues with symmetry decides arbitrarily the correspondence
between the `indistinguishable' atoms. For example, performing TMD using
coordinates of the ring atoms of a PHE, will force the position of atom CD1
in the initial set to move to the position of atom CD1 in the target set,
although the movement from CD1 to CD2 is also possible. In such transitions,
it is likely that there exist a path with a high energy barrier (e.g. flipping
of a PHE ring in a tightly-packed protein interior) that can be avoided by
making use of symmetry. The current method, CONFormational consistency, is an
algorithm for renaming certain atoms to minimize rotation and flipping of
the involved residues during path generation.
Files Added:
source/manip/confcons.src
test/c36test/confcons.inp
Files Modified:
doc/corman.src
build/UNX/manip.mk
..............................................................................
1.2.2 Interpolated path generation
Generate a path between two coordinate sets contained in the main and
comparison coordinates by interpolation. Only linear inrepolation is currently
implemented. The resulting initial path may be used for subsequent path
refinement procedures, such as NEB or TREK.
Files Added:
source/manip/interp_path.src
Files Modified:
build/UNX/manip.mk
doc/corman.src
..............................................................................
1.2.3 Zero-temperature string method
The temperature string method allows the the calculation of minimum
energy paths (MEP) between two conformations of a molecule. The method is
described in
[1] E, W., Ren, W. & Vanden-Eijnden, E. "Simplified and improved string
method for computing the minimum energy paths in barrier-crossing events."
J. Chem. Phys. (2007) 126, 164103-8
Prefx Keys: STRINGM
Files Added:
doc/stringm.doc
source/stringm/reparam.src
source/stringm/splines.src
source/stringm/stats.src
source/stringm/string.src
source/stringm/stringm.src
test/c36test/zts_ens.inp
Files Modified:
install.com
build/UNX/minmiz.mk
build/UNX/objlibs.mk
doc/ensemble.doc
source/fcm/ensemble.fcm
source/io/mainio.src
source/io/coorio.src
source/minmiz/steepd.src
source/util/title.src
------------------------------------------------------------------------------
1.3 Enhancement for SQUANTM combined QM/MM module
Developer : Kwangho Nam and Jiali Gao
Email Address : nam@tammy.harvard.edu; gao@chem.umn.edu
Institution : Harvard University and University of Minnesota
Date : June 25, 2008
1.3.1 Free energy perturbation implementation for pKa calculation
The SQUANTM semiempirical QM/MM module is extended to perform FEP
calculations, in which one application is to compute the pKa value.
The current implementation is that the hybrid Hamiltonian is as
described in pdetail.doc with two Hamiltonians for the reactant and
product states, respectively, and that the reactant state is always
the protonated species and the product state is the deprotonated
species.
1.3.2 Combined use of ab initio QM/MM and semiempirical QM/MM potentials
A so-called multi-layered QM/MM potential is implemented. The basic
idea is similar to the electronically embedded ONIOM type potential. It
computes a QM/MM energy for a large QM region at the semiempirical QM/MM
level, and QM/MM energies for a smaller QM region at the ab initio and
semiempirical QM/MM levels. The difference from the two calculations for
smaller QM/MM region is added to the first QM/MM energy for larger QM
region as a correction for the total energy. The current implementation
is limited to use GAMESS-UK and SQUANTM.
1.3.3 DIIS implementation
In order to improve the SCF convergency, DIIS converger is
implemented, which can be turned off (see qmmm.doc) for the backward
compatibility.
Files Added:
source/squantm/sqnt_mlayer.src
source/squantm/sqnt_pka_fep.src
test/cquantumtest/but4_squantm_pka.inp
test/cquantumtest/lys_mlayer_guk.inp
test/cquantumtest/qmmm_ewald_squantm_pka.inp
test/data/input_lys.guk
Files Modified:
install.com
build/UNX/squantm.mk
doc/qmmm.doc
source/charmm/iniall.src
source/dynamc/dynamc.src
source/dynamc/dynamvv.src
source/dynamc/tmd.src
source/energy/energy.src
source/energy/eutil.src
source/fcm/gamess.fcm
source/fcm/mndo97.fcm
source/fcm/squantm.fcm
source/flucq/flucq.src
source/gener/update.src
source/gukint/gukini.src
source/mc/mvcrot.src
source/mndint/mndewald.src
source/nbonds/ewaldf.src
source/nbonds/nbonds.src
source/nbonds/pme.src
source/pert/epert.src
source/quantum/qmnbnd.src
source/quantum/qub.src
source/squantm/sqnt_ene.src
source/squantm/sqnt_mlayer.src
source/squantm/sqnt_nbnd.src
source/squantm/sqnt_pka_fep.src
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/squantm/sqnt_setup.src
------------------------------------------------------------------------------
1.4 Developments at the National Institute of Health
Institution : Laboratory of Computational Biology, NHLBI, NIH
Date : July 1, 2008
1.4.1 Classical and QM/MM Mobile Block Hessian and MSCAle 2nd derivatives
Developer : H. Lee Woodcock III, Yihan Shao, An Ghysels, Bernard Brooks
Email Address : hlwood@nih.gov, yihan.shao@gmail.com, An.Ghysels@ugent.be,
brb@nih.gov
Added Classical and QM/MM Mobile Block Hessian (i.e. MBH).
Added normal mode support to the MSCAle command. This works with classical
and both ab initio and semi-empirical QM/MM using both analytic and finite
difference second derivatives
minor fix to the printing of off-path simulation results (epath.src)
Prefx Keys: MSCALE, RPATH
Files Added:
source/vibran/mbh.src
Files Modified:
doc/minimiz.doc
doc/mscale.doc
doc/vibran.doc
source/fcm/gamess.fcm
source/dynamc/lonepair.src
source/energy/energy.src
source/energy/epath.src
source/gukint/gukini.src
source/pert/epert.src
source/vibran/vibblock.src
source/vibran/vibran.src
source/build/UNX/vibran.mk
source/mscale/mscale.src
test/c35test/vsa_butane.inp
New/Modified Testcase:
test/c36test/mbh.inp
test/c36test/mbh_partial_opt.inp
test/c36test/vibran_mscale.inp
test/c36test/vsys1.inp
test/c36test/vsys2.inp
..............................................................................
1.4.2 Enhancements and documentation update
Developer : Rick Venable
Email Address : venabler@nhlbi.nih.gov
(1) Pressure tensor data ouptut
In order to capture the pressure tensor data on every integration step
without being overwhelmed by additional data from setting NPRINT 1, the
IUPTEN option was added to the pressure related parsing (prssre.src).
The default is to do nothing unless a positive integer is specified for
this Fortran unit number. Calls to PSCALE() were modified to add the
integration step, so that the time values could be written properly.
Files Modified:
doc/pressure.doc
source/charmm/iniall.src
source/dynamc/prssre.src
source/dynamc/dynamc4.src,
source/dynamc/dynamc.src
source/fcm/reawri.fcm
c24test/nptdyn.inp
(3) crystl.doc update
Updated the information on using image patches with CRYSTAL. Added a
section describing the use of P21 symmetry for interfacial systems, with
some input examples for the coordinate placement, the symmetry change,
and the needed minimization.
Files modified:
doc/crystl.doc
(2) Split trajectory into subsets
Up to 64 subsets may be created from input trajectory files, using a list
which identifies the subset number for each frame in the input trajectory.
The membership list format is that produced by the CLUSTER command of
CORREL, specified by the UNIMember keyword of CLUSTER. Any means may be
used to produce the file, as long as it conforms to that format. The time
base is ignored when writing the subsets, and each is renumbered as a
sequential series from 1 to N, where N is the number of frames in the subset.
Files Modified:
doc/dynamc.doc
source/dynamc/dynsub.src
test/c35test/mrgsubset.inp
..............................................................................
1.4.3 Bugfix for b-spline correction in IPS calculation
Developer : Xiongwu Wu and Bernard Brooks
Email Address : wuxw@nhlbi.nih.gov
The correction to b-spline spreading of atoms is missing, which causes
errors in IPS energy, force and viral calculation.
Files involved:
doc/nbonds.doc Changes in IPS description
source/energy/energy.src Removed NTRANS from AIPS routine argument.
source/fcm/nbips.fcm Added boundary energy variables
source/nbonds/enbips.src B-spline correction is added
------------------------------------------------------------------------------
1.5 University of Michigan Developments
Developer : Jana Khandogin, Charlie Brooks
Email Address : jana.khandogin@ou.edu, brookscl@umich.edu
Institution : U. Oklahoma, U. Michigan
Date : June 30, 2008
1.5.1 Small additions and corrections for pHMD w/ periodic images
Prefx Keys: PHMD
Files Modified:
source/energy/phmd.src
..............................................................................
1.5.2 Additions to tamd to permit multiple roots for TAMD
Developer : Jianhan Chen, Charlie Brooks
Email Address : jianhanc@ksu.edu, brookscl@umich.edu
Institution : KSU, U. Michigan
Changes were made to enable the use of multiple root points in setting
up and running torsion angle molecular dynamics.
Prefx Keys: TAMD
Files Modified:
doc/tamd.doc
source/dynamc/tamd.src
..............................................................................
1.5.3 Fixes and enhancements
Developer : Mike Crowley, Charlie Brooks
Email Address : michael_crowley@nrel.gov, brookscl@umich.edu
Institution : NREL, U. Michigan
Fixes for itanium clusters, em64t, osx, ##IF problems, obsolete fortran,
and column fft codes.
- Fixed MPI communications and pref flags for
- itanium cluster parallel builds
- obsolete flags removed for osx and em64t
- testing parallel with machinefile added
- TESTENDIAN trajectory reading fixed for trajectories with fixed atoms
- Faster direct space fixed (FEWMFC), mkl added
- Code cleanup in pme, bugfix column fft, workaround for bug in intel
compiler affecting fft
- Code constructs that have been deleted from fortran standard, and are
not in intel fortran anymore are replaced with working code.
Prefx Keys: FEWMFC, COLFFT, INTELMKL
Files Modified:
install.com
build/UNX/Makefile_itanium
build/UNX/Makefile_em64t
build/UNX/Makefile_osx
build/UNX/dynamc.mk
source/adumb/umb.src
source/dynamc/dynamc.src
source/dynamc/dynio.src
source/energy/energy.src
source/energy/eintern.src
source/fcm/emap.fcm
source/fcm/blockappend.fcm
source/io/rtfio.src
source/machdep/machutil.src
source/manip/corman2.src
source/misc/gnn.src
source/misc/grid.src
source/misc/gsbp.src
source/misc/gsbp2.src
source/misc/pbeq.src
source/misc/pbeq2.src
source/nbonds/enbond.src
source/nbonds/ewald.src
source/nbonds/nbonds.src
source/nbonds/pme.src
source/nbonds/pme_column_fft.src
source/nbonds/pmeutil.src
source/util/new_timer.src
test/test.com
------------------------------------------------------------------------------
1.6 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, 2008
1.6.1 ETRAJ as a preparation for the CSA module
New CSA module is being introduceds in the CHARMM. The CSA module
itself is not ready for submission yet, but the infrastructure for its
implementation and some other useful functionality is already
finished. ETRAJ command is one of them and it parallelizes reading of
the coordinate sets from the trajectory file and allows to perform any
CHARMM script on individual sets independently. The parallelization is
non-blocking and each of the individual scripts may run in parallel
(Parallel/parallel: similar to QM/MM RPATH calculations) The module is
controlled by #CSA and/or #DISTENE (for ETRAJ) pref.dat keywords.
Files Added:
doc/csa.doc
source/csa/csacntrl.src
source/csa/csacomm.src
test/c36test/csatest.inp
test/c36test/csamin.inp
Files Modified:
build/UNX/objlibs.mk
source/charmm/charmm_main.src
.............................................................................
1.6.2 Conversion of ABNR module to the new fortran
Converted abner.src into the new fortran's module and getting rid
of all the heap and stack usage in abner.src including partial remove
of heap/stack in the dependencies files defining and using the
modified variables. Along with this the major part was converting
FLUCQ, which is almost completely converted to the new fortran, too.
Files Modified:
build/UNX/dynamc.mk
source/charmm/charmm_main.src
source/correl/anacor.src
source/correl/ancsol.src
source/correl/rdfsol.src
source/dynamc/dcntrl.src
source/energy/energy.src
source/energy/intere.src
source/fcm/flucq.fcm
source/flucq/flucq.src
source/flucq/fluqdyn.src
source/flucq/fluqene.src
source/flucq/fluqqmmm.src
source/image/upimag.src
source/image/xtlfrq.src
source/io/trajio.src
source/manip/scalar.src
source/mbond/mbdiag.src
source/mc/mcimge.src
source/minmiz/abner.src
source/minmiz/conjug.src
source/minmiz/egrad1.src
source/minmiz/minmiz.src
source/minmiz/nraph.src
source/minmiz/powell.src
source/minmiz/steepd.src
source/minmiz/tndriv.src
source/misc/distrib.src
source/misc/genetic.src
source/misc/grid.src
source/misc/hbuild.src
source/nbonds/cheqmodule.src
source/nbonds/nbonds.src
source/pert/epert.src
source/pert/icfcnf.src
source/pert/icpert.src
source/pert/tsme.src
source/quantum/qmevdw.src
source/util/selcta.src
source/vibran/vibcom.src
.............................................................................
1.6.3 REPDSTR enhancements
Some fixes for distributed replica functionality and added
support for the Off Path Simulation method:
Files Modified:
source/charmm/miscom.src
source/energy/energy.src
source/energy/epath.src
source/gener/repdstr.src
source/minmiz/abner.src
.............................................................................
1.6.4 pref.dat and other fixes
Some fixes for ##IF statement and other problems:
Files Modified:
install.com
source/mscale/mscale.src
source/nbonds/enbips.src
source/nbonds/nbutil.src
source/nbonds/pmeutil.src
.............................................................................
1.6.5 GAMESS/CHARMM QM/MM interface: support for the latest GAMESS
Support for latest version of GAMESS (11 Apr 2008 R1) released on
April 21, 2008 was added to CHARMM. New development in this version
includes: new grid code for DFT calculations (the default has changed
- so are the results if compared with older version). Popular SG1 was
added.
Files Modified:
build/UNX/gmscomp
doc/gamess.doc
------------------------------------------------------------------------------
1.7 Michigan State University Developments
Developer : Sean Law, Srinivasa Murthy Gopal/Michael Feig
Email Address : feig@msu.edu
Institution : Michigan State University
Date : June 28, 2008
1.7.1 1D and 2D PMF-based potentials
A series of PMF-based potentials is introduced to faciliate the
development of coarse-grained models. The potentials consist of three
different modes: 1D distance, 2D angle, and 2D hydrogen-bonding term.
Prefx Keys: EPMF
Files Added:
doc/epmf.doc
source/energy/epmfmodule.src
test/c36test/epmf.inp
test/data/epmf1d.dat
test/data/epmf2d.dat
Files Modified:
install.com
build/UNX/energy.mk
source/charmm/charmm_main.src
source/energy/eutil.src
source/energy/energy.src
source/energy/ecnstr.src
source/energy/printe.src
source/energy/ecmap.src
source/fcm/energy.fcm
..............................................................................
1.7.2 Variable distance center of mass restraint
An option was added to the HMCM module to allow a restraint with an
arbitary distance between the reference center of mass and actual center
of mass (rather than the default zero distance).
Prefx Keys: part of HMCM
Files Modified:
doc/cons.doc
source/energy/energy.src
source/energy/ecnstr.src
source/fcm/cnst.fcm
source/manip/cstran.src
source/pert/epert.src
..............................................................................
1.7.3 3D path-based restraint
A biasing potential that restraints the projection of selected
centers of mass along a spline-interpolated, three-dimensional path.
This potential is especially useful for DNA translocation.
Prefx Keys: CPATH
Files Added:
test/c36test/conspath.inp
test/data/nt4.pdb
test/data/splinepts.inp
Files Modified:
install.com
doc/cons.doc
source/charmm/iniall.src
source/energy/eutil.src
source/energy/energy.src
source/energy/ecnstr.src
source/energy/printe.src
source/fcm/cnst.fcm
source/fcm/energy.fcm
source/fcm/dimens.fcm
source/manip/cstran.src
..............................................................................
1.7.4 GBMV and HDGB improvements
The possibility to define atom-specific surface tension coefficients akin
to an ASP term is introduced into GBMV. The previously fixed functional form
for the non-polar profile in the HDGB model is extended to allow an arbitrary,
spline-interpolated profile based on input from an external file. In addition,
there are a few very minor changes and fixes.
Prefx Keys: GBMV
Files Modified:
doc/gbmv.doc
source/energy/gbmvmodule.src
..............................................................................
1.7.5 Miscellaneous changes and fixes
A number of small changes are summarized here:
- changed optimization level and modified CMAP code to avoid numerical errors
on 64-bit Intel architecture.
- fixed name conflict in VIBBLOCK module (pythag subroutine)
- allow extended PSF format for XPLOR format (needed for NAMD interaction)
Files Modified:
build/UNX/energy.mk
build/UNX/Makefile_em64t
source/energy/ecmap.src
source/io/psfres.src
source/vibran/vibblock.src
------------------------------------------------------------------------------
1.8 HYBH: HYBrid Hamiltonian module
Developer : Arnaud BLONDEL
Email Address : ablondel@pasteur.fr
Institution : Institut Pasteur (Paris, France)
Date : June 30, 2008
Implementation of the truncation scheme described in "Ensemble Variance
in Free Energy Calculations by Thermodynamic Integration: Theory, Optimal
"Alchemical" Path, and Practical Solutions", A.Blondel (2004) J.Comp.Chem 25,
985-993. Details on the method should be sought therein. In brief, the
implementation is based on dual topology (although single topology
could be used under some conditions), the bonded terms (bond, angle
and Urey-Bradly) are kept unchanged, dihedral and impropers are
modified according to simple quadratic scheme (w_product=(3.l+1).l/4),
and electrostatic and van der Waals are treated together with a
truncation scheme reminiscent of soft-core vdw to minimize the
numerical fluctuations of the integrant (hence Optimal "Alchemical"
Path). Ewald sums and correction terms associated appeared soft
enough to be treated according to linear scaling of the charges,
allowing direct analytical calculation of dEwald/dl. A benefit of the
method, in addition to the fact that the integrant has limited
numerical fluctuations, is that it also produce a linear evolution of
the integrant along lambda (or l) in regular cases.
The implementation attempts to supports most of non-bonds, image
and Ewald sums options and warnings are made. Slow routines are not
currently supported. However, it is advised to test the results when
new combination of options are used. CMAP is not currently supported.
No analysis routine is currently supplied as careful convergence
analysis should be undertaken. It is advised that additions of the
terms be made at least in real*8 format as truncation errors might
be significant otherwise.
Prefx Keys: BLOCK
Files Added:
source/fcm/trunk.fcm
test/c36test/block_hybh.inp
test/c36test/block_hybh_ew.inp
Files Modified:
doc/block.doc
source/charmm/iniall.src
source/dynamc/dynamc4.src
source/dynamc/dynamc.src
source/dynamc/dynamcv.src
source/dynamc/dynamvv.src
source/dynamc/dynamvv2.src
source/dynamc/dynamln.src
source/energy/energy.src
source/energy/enefscal.src
source/energy/eintern.src : Ref. added for ephi.
source/fcm/block.fcm
source/fcm/energy.fcm
source/image/eimage.src
source/mc/mvcrot.src : Fix - CROSS renamed VPROD (vectorial product)
source/nbonds/enbfast.src
source/nbonds/enbond.src
source/nbonds/ewald.src
source/nbonds/enbaexp.src
source/nbonds/nbonds.src
source/nbonds/pme.src
source/pert/block.src
------------------------------------------------------------------------------
1.9 Arizona State University Developments
Developer : Hiqmet Kamberaj and Arjan van der Vaart
Email Address : hkamberaj@asu.edu and vandervaart@asu.edu
Institution : Arizona State University
Date : June 27, 2008
1.9.1 Replica Exchange Using Tsallis Statistics
Molecular dynamics using Tsallis scaling of the CMAP and Dihedral
potential terms can now be performed. This method is implemented for all
integrators (dynamc.src). The method for Tsallis scaling of the CMAP and
Dihedral potential terms is invoked by adding to the DYNAmics command the
keywords: TTSALlis QTSAllis real EMIN real, where QTSAllis is the Tsallis
q and EMIN is the estimated minimum energy of the CMAP + Dihedral terms,
having similar meaning as for TSALLIS. The default value of QTSAllis is 1,
in which case the method reduces to standard dynamics (no scaling). Values
of q larger than 1 effectively correspond to a smoothed potential in which
the positions of the extrema are preserved. Estimates for EMIN should be
lower than any possible energy of the CMAP+Dihedral potential terms
encountered during the simulation.
It is important to note that the scale factor for the forces involves
a temperature. The temperature employed in the Tsallis transformation
corresponds to the one used to assign the velocities during heating and
equilibration (TSTRUC initially and then FIRSTT + int*TEMINC). Thus, it is
important to set FIRSTT, FINALT and TEMINC appropriately even if one is
running Langevin dynamics at temperature TBATh (i.e., for equilibrium
dynamics, set FIRSTT = FINALT = TBATh). Furthermore, simple scaling of the
CMAP and Dihedral potential terms can also be performed by adding to the
DYNAmics command the keywords: POTSaling TSALpha, where TSALpha is the
scaling factor of the CMAP + Dihedral terms. The default value of TSALpha
is 1, in which case the method reduces to standard dynamics (no scaling).
Values of Alpha smaller than 1 correspond to a smoothed potential.
Reference: H. Kamberaj and A. van der Vaart (2007) Multiple Scaling Replica
Exchange for the Conformational Sampling of Biomolecules in Explicit Water.
J. Chem. Phys., 127, 234102-7.
BLOCK was modified so that it works with the Ewald (simple and PME)
method of CHARMM. The Syntax and Function of BLOCK module are unchanged.
Files Added:
source/energy/tsallismodule.src
test/c36test/pme_block.inp
test/c36test/tsallis.inp
Files Modified:
doc/block.doc.
doc/dynamc.doc
build/UNX/charmm.mk
build/UNX/energy.mk
source/charmm/charmm_main.src
source/dynamc/dcntrl.src
source/energy/ecmap.src
source/energy/ecntrl.src
source/energy/enefscal.src
source/energy/energy.src
source/energy/printe.src
source/nbonds/pme.src
source/nbonds/nbonds.src
source/nbonds/ewald.src
source/nbonds/enbaexp.src
..............................................................................
1.9.2 Simple Ewald method for any simulation box shape.
Simple Ewald method is modified to run for every simulation box shape.
In additional, BLOCK was modified so that it works with the Simple Ewald
method of CHARMM. The Syntax and Function of BLOCK module are unchanged.
Files Modified:
doc/nbonds.doc
source/nbonds/ewaldf.src
------------------------------------------------------------------------------
1.10 RCONS Improvements
Developer : Jhih-Wei Chu
Email Address : jwchu@berkeley.edu
Institution : UC Berkeley
Date : June 29, 2008
The efficiency and robustness of the algorithm for maintaining
equal-distance constraints are improved significantly. New restraint
potentials are added in epath to help cotrolling path smoothness and
obtain minimium Hamiltonian path
Prefx Keys: RXNCONS
Files Modified:
doc/replica.doc
source/energy/epath.src
source/dynamc/dynamc.src
source/fcm/path.fcm
source/fcm/rxncons.fcm
source/fcm/rxnconswt.fcm
source/fcm/rxncons4.fcm
source/manip/holonom.src
source/manip/rxcons.src
source/manip/rxcons_3.src
source/manip/rxcons_4.src
source/manip/scalar.src
test/c35test/rxncons_rpath.inp
------------------------------------------------------------------------------
1.11 Karolinska Institute Fixes and Enhancements
Developer : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska Institute
Date : June 28, 2008
Added -1 warning if ISEED is specified at a langevin dynamics restart.
Fixed problems with PDB format introduced in c35a2, both for coordinates and
sequences.
Files Modified:
doc/io.doc
source/dynamc/dcntrl.src
source/io/coorio.src
source/io/mainio.src
source/io/psfres.src
------------------------------------------------------------------------------
1.12 University of Chicago Developments
Developer : Haibo Yu, Yuqing Deng, Wei Jiang, Benoit Roux
Email Address : haibo@uchicago.edu, deng@mcs.anl.gov, wjiang@mcs.anl.gov,
roux@uchicago.edu
Institutions : University of Chicago, Argonne National Lab
Date : June 30, 2008
1.12.1 New Format for PSF of Drude Mode
XPLOr format for PSF of Drude mode is extended to include the Thole
and polarizability for each particle. In the new format, the
anisotropic information for the lone-pairs of Drude model is shown
along with the lone-pair information. This new format is intended to
provide a PSF of Drude mode for developing NAMD package.
The parmfile read-in subroutine has been modified to allow ATOM
NAMES longer than 4 characters in NBFIX section (i.e. for DRUDe atoms).
Files Modified:
source/fcm/dimens.fcm
source/io/psfres.src
source/io/parmio.src
..............................................................................
1.12.2 Various updates and enhancement
Problems with SSBP parallel running are fixed.
Fixed a bug in when CAVIty potential is activated in GSBP, and GCMC
simulations are performed. The cavity potential does not go to properly
zero for GCMC solvent molecules inside the sphere for cavity radius
larger than 18 angstroms. This only affects GCMC simulations with GSBP
CAVIty potential activated.
Fixed a bug when the EMPI empirical corrections are activated in a
deformable boundary.
Files Modified:
source/misc/gsbp.src
source/misc/ssbp.src
------------------------------------------------------------------------------
1.13 University of Maryland Developments
Developer : Olgun Guvench, Kenno Vanommeslaeghe and Alex MacKerell
Email Address : alex@outerbanks.umaryland.edu
Institution : University of Maryland, Baltimore
Date : June 30, 2008
1.13.1 Document updates
Lone pairs with undefined coordinates can be built by COOR SHAKE.
Wrong definition of impropers can have problematic results. Clarified this
in the documentation. Also included a warning pertaining the phase of ordinary
dihedrals.
Files involved:
doc/corman.doc
doc/lonepair.doc
doc/parmfile.doc
doc/rtop.doc
..............................................................................
1.13.2 CHARMM General Force field.
The new CHARMM General Force Field, developed in the MacKerell lab and
ready to be published, overflows hard-coded array sizes for dihedrals and
residues. A new preflx keyword, CGENFF, was introduced to request larger
arrays at compile time. As the change has little effect on CHARMM's memory
footprint, install.com was modified to include the CGENFF keyword by default.
All this is consistent with previous additions of "large" force fields
(eg. MMFF). The CGENFF keyword was also added to preflx_list.doc.
Prefx Keys: CGENFF
Files Added:
test/c35test/cgenff.inp
test/data/top_cgenff_all_1g5merge.inp
test/data/par_cgenff_all_1g5merge.inp
Files Modified:
install.com
doc/preflx_list.doc
source/fcm/dimens.fcm
..............................................................................
1.13.3 Added substitution parameters for ring pucker calculation
Added substitution parameters for ring pucker calculation in corman.src.
Files Modified:
doc/subst.doc
source/manip/corman.src
..............................................................................
1.13.4 toppar Updates
Inclusion of initial release of the CHARMM general force field in
the toppar directory. CHARMM general force field has been designed to
treat a range ofpharmacological compounds. The parmaeters have been
optimized to be consistent with the CHARMM all-atom additive force
fields.
Removed:
toppar/par_all34_ethers.prm
toppar/par_all35_sugar.prm
toppar/top_all34_ethers.rtf
toppar/top_all35_sugar.rtf
Files Added:
toppar/par_all32_lipid.prm
toppar/par_all35_carb.prm
toppar/par_all35_ethers.prm
toppar/par_all36_cgenff.prm
toppar/top_all32_lipid.rtf
toppar/top_all35_carb.rtf
toppar/top_all35_ethers.rtf
toppar/top_all36_cgenff.rtf
Updates:
toppar/drude.tar.gz
toppar/silicates.tar.gz
toppar/toppar_history.tar.gz
Files Modified:
toppar/non_charmm/00readme
toppar/par_all27_lipid.prm
toppar/par_all27_na_lipid.prm
toppar/par_all27_prot_lipid.prm
toppar/par_all27_prot_na.prm
toppar/stream/toppar_all27_na_model.str
toppar/top_all27_lipid.rtf
toppar/top_all27_na_lipid.rtf
toppar/top_all27_prot_lipid.rtf
toppar/toppar_all.history
------------------------------------------------------------------------------
1.14 Multiple Energy Evaluation
Developer : Bruce Tidor
Email Address : tidor@mit.edu
Institution : Massachusetts Institute of Technology
Date : July 31st, 2008
The MuLTE command rapidly computes energetics between alternative
conformations of side chain pairs. Cartesian coordinates for a collection
of coordinates for two sets of atoms are stored in "write coor dumb" format
in files read on input. The energy for all conformational pairings are
computed and printed to a specified file.
Files Added:
source/energy/multe.src
test/c36test/multe.inp
Files Modified:
build/UNX/energy.mk
doc/energy.doc
source/charmm/charmm_main.src
source/energy/intere.src
source/misc/grid.src
source/util/chutil.src
------------------------------------------------------------------------------
1.15 Random Number Generator
Developer : Youngdo Won
Email Address : won@hanyang.ac.kr and won@helix.nih.gov
Date : August 6, 2008
As some simulations expand over several nano seconds, recurrence of
random numbers could be a problem. We addressed this with a "new" random
number generator in the version c28a4 (February 15, 2001): the Combined
Linear Congruential Generator (CLCG). It was parallelized in c32a1 (2004).
Problems involved with it were fixed in c33a1 (2005). The CLCG random number
has been default for the special versions compiled with the ##NEWRNG
key. The CLCG code is now default and ##NEWRNG encapsulation is removed.
For testing or checking previous trajectories, the "old" random number
generator, REAL* FUNCTION OLDRANDOM(ISEED), is available as a run time option.
In order to switch the "old" random number generator, the miscellaneous
RANDom command is modified to include,
RANDom [OLDRandom ]
[CLCG ]
Files Modified:
install.com
doc/miscom.doc
source/charmm/iniall.src
source/correl/solana.src
source/dynamc/dcntrl.src
source/dynamc/dims.src
source/dynamc/dynamc.src
source/dynamc/dynio.src
source/dynamc/dynlng.src
source/dynamc/dynutil.src
source/fcm/exfunc.fcm
source/fcm/rndnum.fcm
source/manip/intcor.src
source/mc/mc.src
source/misc/genetic.src
source/misc/pbeq.src
source/util/clcg.src
source/util/random.src
source/vibran/vibran.src
------------------------------------------------------------------------------
1.16 Bugfixes and Enhancements
1.16.1 VMOD fixes
Developer : Charles Robert (& David Perahia)
Email Address : charles.robert@u-psud.fr
Institution : CNRS - France
Date : May 19, 2008
In the previous version VMOD used its own normal-mode file-reading
routine that was incomplete. Several new features have been added as well.
VMOD obtains the restraint direction(s) from a normal-mode format file.
In the initial version, an over-simplified approach was used to read the
file. To resolve this and potentially other future problems, VMOD now re-uses
existing code from VIBRAN for reading the normal-mode file. This provides
the advantage of guaranteeing VMOD/VIBRAN coherence in the future.
Files involved:
doc/mmfp.doc
source/energy/energy.src
source/fcm/mmfp.fcm
source/misc/mmfp.src
source/vibran/vibio.src
test/c34test/vmodwat.inp
..............................................................................
1.16.2 VIBRAN READ NORM
Developer : Charles Robert (& David Perahia)
Email Address : charles.robert@u-psud.fr
Institution : CNRS - France
Date : May 19, 2008
In VIBRAN, one should be able to read normal modes from either a binary
or card-formatted normal modes file. Further, the READ NORM command allows
one to specify which modes are to be read from the file, e.g., mode 7 from
a file with 20 modes. Call this reading from the "middle" of the file.
There are no problems when all modes are read at once for either binary or
card-formatted files. Also, a single mode can be read from the middle of a
binary file without any problem. But for reading one or more modes from the
middle of a card formatted file, the wrong values are obtained.
Files involved:
source/vibran/vibio.src
..............................................................................
1.16.3 Bug fixed in FACTS image interaction list setup
Developer : Francois Marchand and Amedeo Caflisch
Email Address : caflisch@bioc.uzh.ch
Institution : Department of Biochemistry, University of Zurich
Date : June 30, 2008
FACTS builds lists for the atom-atom and atom-image atom interactions.
The size of the image atom array (equivalent to NATIM) was set to be
twice the number of atoms present in the system. It appeared that
the actual number of image atoms can be bigger than that, what leads
to crashes under certain system configurations.The size of this array
was set to 26*NATOM instead of 2*NATOM.
Files involved:
doc/facts.doc
source/image/images.src
source/misc/fctall.src
..............................................................................
1.16.4 DIMS one-line bugfix
Developers : Juan R. Perilla, Oliver Beckstein, Anu Nagarajan,
Jennifer Johnston, Elizabeth Denning, Tom Woolf
Email Address : jrperillaj@jhu.edu, orbeckst@jhmi.edu, anu@jhu.edu,
jen.johnston@jhmi.edu, edennin3@jhu.edu, twoolf@jhmi.edu
Institution : Johns Hopkins University, School of Medicine
Date : June 30, 2008
ntres=ntres+1 added.
Files involved:
source/dynamc/dims.src
..............................................................................
1.16.5 CORSOL f95 compilation
Developer : Tibor Rudas and Stefan Boresch
Email Address : tibor.rudas@univie.ac.at, stefan@mdy.univie.ac.at
Institution : University Vienna
Date : Jun 28th 2008
Compilation of CHARMM failed when the CORSOL keyword was present
in pref.dat for several reasons: (i) Change of the CHEQ functionality
to Fortran95 required the additon of 'use cheq...'.
(ii) During the Fortran95 migration, an assigned goto was handled
incorrectly. By mimicking what was done in correl.src the problem could
be avoided
Files involved:
source/correl/corsol.src
source/correl/ancsol.src
..............................................................................
1.16.6 RMD documentation update
Developer : Stephan Lutz
Email Address : stephan.lutz@unibas.ch
Institution : University of Basel, Switzerland
Date : 06/30/2008
Some remarks added to the RMD documentation (cross.doc) concerning
the configuration of the supplied PSF when using the RXMD command.
Files Modified:
doc/cross.doc
..............................................................................
1.16.7 PNM gradient calculation
Developer : Jingzhi Pu
Email Address : pu@tammy.harvard.edu
Institution : Harvard University
Date : july 15, 2008
Introduced into CHARMM since c35a1, the PNM code was adopted from
a preliminary code as a part of the USER command. Since the energy routine
for USER energy (subroutine USERE) was called at the very beginning of all
energy components, the PNM gradients were directly assigned to their global
arrays (DX,DY,DZ). However, PNM gradients should be incorporated
accumulatively. The bug actualy does not affact the results for most of
the calculations, except for a few rare cases, for example, when the
USER or RXMD command is used in combination with the PNMI command.
Files involved:
source/misc/pnm.src
..............................................................................
1.16.8 GHO atom parameters for GHO-MNDO/d
Developer : Jingzhi Pu
Email Address : pu@tammy.harvard.edu
Institution : Harvard University
Date : july 15, 2008
A bug is found in source/mndint/mndo97q/97/PARAMD.f. The GHO atoms in
the CHARMM/MNDO97 interface are conviniently defined as an element
with atom number 85. Paramters for GHO are therefore adopted from
carbon by mapping parameters of the element 85 to those of the element 6.
However, for the MNDO/d Hamiltonian, due to the structure of the code,
at some point, following 'DO 50 I=11,LMD' in the subroutine PARAMD of
source/mndint/mndo97q/97/PARAMD.f, the GHO parameters are reset to the
original MNDO/d parameters for the real element 85 (which is actually
missing in the parameter definition). So we explicitly skip this reassignment
if a GHO atom is detected (I .eq. 85), to prevent it from being overwritten.
Files involved:
source/mndint/mndo97q/97/PARAMD.f
The following are introduced and modified during the development period
of August 15, 2008 through February 15, 2009. The developments are
based on CHARMM version c36a1. As F95 conversion is in progress, we include
minor enhancements and fixes into c36a2. On going developments will be
incorporated into the fully converted version of c36a1x, to be available by
May 15, 2009.
2.1 University of Maryland Developments
Developer : Igor Vorobyov, Guillaume Lamoureux and Alex MacKerell
Email Address : ivorobyov@ucdavis.edu, guillaume.lamoureux@concordia.ca
and alex@outerbanks.umaryland.edu
Institution : University of Maryland, Baltimore
Date : December 31, 2008
2.1.1 MMFP bugfixes
(1) Output to MMFP data file was incorrectly handled if running CHARMM
code on more than 2 cpus. The MMFP constraint calculation and data
output at each time step was handled on a different cpu from the one
used for the other data I/O. The cpu or node asignment used for these
calculations depended on the number of processors used for
calculations. Therefore, the code was modified to always run on cpu
(node) 0 i.e. the same one used for I/O as well.
(2) Unnecessary information was printed to MMFP data file at each step
of the simulation, namely "Angle : ", "Dihedral: " or "R : ". These
were removed to save space.
(3) There were duplicate entries in MMFP data files associated with the
calculation of system energy at the end and the beginning of each
block of molecular dynamics within the same DYNAmics run. The block
length might correspond to the frequency for stopping the rotation and
translation of the system (NTRFRQ) or step frequency for calculating
averages and standard deviations (IPRFRQ). These duplicate entries
were removed by using QMMFPW logical variable, which is set to be true
if writing to MMFP data file is allowed.
Files involved:
source/energy/energy.src (1)
source/dynamc/dcntrl.src (3)
source/fcm/contrl.fcm (3)
source/misc/mmfp.src (2)
..............................................................................
2.1.2 TPCONTROL for monoclinic ('MONO') crystal types
The 'FULL' option in TPCONTROL now accepts monoclinic ('MONO') crystal
types. The following crystal types are now available for constant-pressure
dynamics with a fully flexible cell: CUBI, RECT, OCTA, RHDO, ORTH, MONO, TRIC.
Still not tested (but possibly working) are: TETR, HEXA, RHOM.
Files involved:
dynamc/dynamvv2.src
..............................................................................
2.1.3 Eight character RESIdue name support
There appears to be a small bug with the number of characters
recognized by the "read sequence RESI NRES" command. When you have a
residue with more then 4 characters "read sequence RESI NRES" only
recognizes 4 characters in the residue name. This leads to the
generate statement failing as it can't find the correct residue in the
topology. Using "read sequence card" does not give this error.
Files involved:
source/io/mainio.src
------------------------------------------------------------------------------
2.2 RMD fixes and enhancements
Developer : Stephan Lutz, Markus Meuwly
Email Address : stephan.lutz@unibas.ch, m.meuwly@unibas.ch
Institution : Department of Physical Chemistry, University of Basel
Date : December 26, 2008
Several modifications in Reactive MD module removing some bugs found for
very specific PSF and RMD definitions. Additionally, the previous precondition
for a mandatory bond inclusion in the PSF when the specific bond is getting
removed in the RMD definition is now abolished. Merged all Fortran77 COMMON
BLOCK variables from cross.fcm into module cross and converted all fixed size
arrays to allocatable ones.
Files Removed:
source/fcm/cross.fcm
Files Modified:
build/UNX/charmm.mk
build/UNX/dynamc.mk
build/UNX/energy.mk
build/UNX/misc.mk
build/UNX/pert.mk
doc/cross.doc
source/charmm/iniall.src
source/charmm/miscom.src
source/dynamc/dcntrl.src
source/dynamc/dynamc.src
source/energy/energy.src
source/misc/cross.src
source/misc/genetic.src
source/pert/epert.src
source/pert/icpert.src
test/c35test/cross.inp
------------------------------------------------------------------------------
2.3 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 31, 2008
2.3.1 Overlap method is modularized
The Overlap method is now in the module. The same code was ported
to c36a1x development.
Files Modified:
build/UNX/energy.mk
source/charmm/charmm_main.src
source/charmm/miscom.src
source/energy/energy.src
source/energy/eolap.src
source/fcm/olap.fcm
source/misc/olap.src
.............................................................................
2.3.2 GRAPE interface in CHARMM extended to support GPU cuda library.
The interface code in CHARMM to the GRAPE library was extended so
it supports also the GPU (cuda library).
Files Modified:
source/charmm/iniall.src
source/fcm/grape.fcm
source/nbonds/enbond.src
source/nbonds/grape.src
source/nbonds/nbutil.src
source/nbonds/pme.src
.............................................................................
2.3.3 REPDSTR fixes and enhancement
The distributed replica method was enhanced by few more commnads
so it allows communication between chosen replicas in a CHARMM script
itself. The new commands are repd sync, repd iores, repd ioset. See
doc/repdstr.doc file for more info.
Files Modified:
doc/repdstr.doc
source/fcm/repdstr.fcm
source/gener/repdstr.src
source/io/coorio.src
source/io/mainio.src
source/machdep/machio.src
source/machdep/paral1.src
source/machdep/paral2.src
source/util/parse.src
.............................................................................
2.3.4 Smaller miscellaneous fixes and enhancement
There was an unprotected call to communication in the energy
routine: it is now properly protected. Several fixes were needed to
compile CHARMM LITE version. Some comment lines were added in cstuff.c
for future development of the routines in that source file. And one
subroutine name conflict was resolved.
Files Modified:
install.com
source/energy/energy.src
source/flucq/flucq.src
source/flucq/fluqdyn.src
source/flucq/fluqene.src
source/flucq/fluqqmmm.src
source/machdep/cstuff.c
source/manip/confcons.src
------------------------------------------------------------------------------
2.4 Updates on reaction path constraint facilities
Developer : Jhih-Wei Chu
Email Address : jwchu@berkeley.edu
Institution : UC Berkeley
Date : December 23, 2008
Bug fixes and minor enhancement on the reaction path facilities.
Files Modified:
source/dynamc/dynamc.src
source/energy/epath.src
source/fcm/rxncons3.fcm
source/fcm/rxncons4.fcm
source/fcm/rxncons.fcm
source/manip/holonom.src
source/manip/rxcons.src
source/manip/rxcons_3.src
source/manip/rxcons_4.src
------------------------------------------------------------------------------
2.5 Bugfixes and Enhancements
2.5.1 VV2 Bugfix for NVT ensemble runs
Developer : Haibo Yu and Benoit Roux
Email Address : haibo@uchicago.edu and roux@uchicago.edu
Institutions : University of Chicago, Argonne National Lab
Date : September 6, 2008
Simulations with VV2 integrator at NVT ensemble crash at step 0
with an error mesg SHAKE failed. Some of the variables in RattleRoll
subroutine are not initialized.
Files involved:
source/dynamc/dynamvv2.src
..............................................................................
2.5.2 AM/MM atom selection for link atoms
Developer : H. Lee Woodcock III and Bernard R. Brooks
Email Address : hlwood@nih.gov and brb@nih.gov
Institution : Laboratory of Computational Biology, NHLBI, NIH
Date : December 31, 2008
Due to the extension of the Q-Chem QM/MM interface to handle QM/MM
Hessian with link atoms the atom selections based on IGMSEL needed
to be modified to include link atoms.
Files involved:
source/gukint/gukini.src
------------------------------------------------------------------------------
2.5.3 REPDSTR and ADDLink bugfixes
Developer : Kwangho Nam
Email Address : nam@tammy.harvard.edu
Institution : Harvard University
Date : December 30, 2008
A error has fixed in the replica exchange method using
REPDstr module. In the module, the exchange between two
neighboring replicas occurs when the exchange probability
is larger than random number, but the bug results in the
reversed decision, and this bug is fixed.
For the ADDLink keyword, we fix it to include SQUANTM
module.
Files involved:
source/charmm/charmm_main.src
source/gener/repdstr.src
..............................................................................
2.5.4 MCMA code updated
Developer : Peter Steinbach
Email Address : steinbac@helix.nih.gov
Institution : CMM/DCB/CIT, National Institutes of Health
Date : October 17, 2008
PRNLEV control is activated and MAINCOMX is used in the main routine.
Files involved:
source/mc/mcma.src
..............................................................................
2.5.5 The mass array scaling kept unchanged for the force constant
Developer : nuria plattner
Email Address : nuria.plattner@unibas.ch
Institution : University of Basel
Date : October 14, 2008
For path integral molecular dynamics, the force constant between the
beads depends on the mass of the corresponding atoms. The mass is taken from
the AMASS(*) array. At the same time, the mass of the beads used for the
dynamics is scaled by the number of beads. (According to the centroid
approximation.) The two usages of the mass array require different values
of the masses, therefore it is not possible to use only one array for both
modules.
Files involved:
source/energy/pathint.src
source/fcm/pathint.fcm
..............................................................................
2.5.6 Ewald code fixes for HYBrid Hamiltonian module
Developer : Arnaud BLONDEL
Email Address : ablondel@pasteur.fr
Institution : Institut Pasteur (Paris, France)
Date : August 28, 2008
Some conflicts with the existing Ewald/Block implementation are fixed.
Files involved:
source/energy/energy.src
source/nbonds/enbaexp.src
source/nbonds/ewald.src
test/c36test/block_hybh.inp
test/c36test/block_hybh_ew.inp
The following are introduced and modified during the development period
of February 15, 2009 through August 15, 2009. The developments are
based on CHARMM version c36a2. As F95 conversion is in progress, we include
minor enhancements and fixes into c36a3. On going developments will be
incorporated into the fully converted version of c36a1x, to be available by
October 15, 2009.
3.1 University of Chicago Developments
Name : Wei Jiang, Haibo Yu, Benoit Roux
Email Address : wjiang@mcs.anl.gov, haibo@uchicago.edu, roux@uchicago.edu
Institutions : University of Chicago, Argonne National Lab
Date : June 30, 2009
3.1.1 Drude Polarizable Model Related Development
3.1.1.1 Additional Anharmonic Stretching for Drude Particles:
In additional to the harmonic stretching of the Drude particles, one
additional anharmonic stretching is introduced which is necessary for highly
polarizable anions. This function is activated in GENE command with the logical
variable HYPE. Currently all the Drude particles are assigned with the same
anharmonic stretching. The formula is
E_{anharm} = KHYP*(DeltaR - RHYP)**HORD when DeltaR > RHYP.
Files Modified:
source/fcm/psf.fcm
source/gener/drude.src
source/gener/genpsf.src
source/energy/energy.src
source/pert/epert.src
3.1.1.2 Langevin Thermostats for Drude Particles
The Langevin thermostat is further applied to Drude particles (relative
motion of a Drude pair), in addition to the existing Langevin thermostat applied
to center of mass of a Drude-nucleus pair.
Files Modified:
source/dynamc/dynamvv2.src
3.1.1.3 New Format for PSF of Drude Mode
Besides the XPLOr format updated in c36a1, PSF format of Drude model is
extended to include the Thole and polarizability for each particle. In the new
format, the anisotropic information for the lone-pairs of Drude model is shown
along with the lone-pair information.
Files Modified:
source/io/psfres.src
..............................................................................
3.1.2 Enhancement Related to Free Energy Simulations
3.1.2.1 Parallelized MC module
The MC module is parallelized by modifying the non-bonded list when multiple
processors are invoked. For simulation with single CPU, the existing miniature
list is invoked, while for multiple processors, the full non-bonded list same as
a MD simulation is used.
Files Modified:
source/mc/mc.src
source/mc/mvgcmc.src
3.1.2.2 Hamiltonian Replica-Exchange Scheme
The Hamiltonian Replica-Exchange scheme is introduced to the REPDSTR module.
This enables a straightforward replica-exchange for free energy perturbation,
umbrella sampling, and alternative replica-exchange for Hamiltonian-exchange and
parallel tempering.
Files Modified:
doc/repdstr.doc
source/fcm/parallel.fcm
source/fcm/repdstr.fcm
source/gener/repdstr.src
source/dynamc/dcntrl.src
source/manip/cstran.src
..............................................................................
3.1.3 Various Updates and Enhancements
3.1.3.1 CHARMM Installation on BG/P Cluster
The installation and compilation of CHARMM on IBM Blue Gene/P cluster.
Files Modified:
install.com
build/UNX/Makefile_gnu
source/machdep/cstuff.c
3.2 Bugfix related with PERT parallel running
Problems with PERT MMFP parallel running are fixed.
Problems with PERT Drude system parallel running are fixed.
Files Modified:
source/pert/epert.src
------------------------------------------------------------------------------
3.2 Bugfixes/Improvements for SCC-DFTB/MM Options
Name : Qiang Cui, Xiao Zhu
Email Address : cui@chem.wisc.edu, xzhu@chem.wisc.edu`
Institution : University of Wisconsin Madison
Date : June 2009
3.2.1 SCC-DFTB/MM-eWald simulations
The Ewald summation with SCC-DFTB/MM is sped up by tabulating the erfc
calculaiton as in pure MM calculations and re-implementing the pre-calculated
terms. With the CUTF option, now SCC-DFTB/MM-eWald simulations are similar in
speed as cutoff based simulations.
Files Added:
source/sccdftbint/sccdftbsrc/gammamat.src
Files Removed:
source/sccdftbint/sccdftbsrc/gammamat.f
Files Modified:
build/UNX/sccdftb.mk
doc/sccdftb.doc
source/sccdftbint/sccdftbini.src
source/sccdftbint/sccdftbsrc/eglcao.f
source/sccdftbint/sccdftbsrc/externalshift.f
source/sccdftbint/sccdftbsrc/externalchgrad.src
source/sccdftbint/sccdftbsrc/long_range.f
source/sccdftbint/sccdftbsrc/long_sccmm1.src
source/sccdftbint/sccdftbsrc/ktable_ewscc.src
..............................................................................
3.2.2 SCC-DFTB/PB function
The added function also works for SCC-DFTB/MM; Allows for charge-dependent
radii (G. Hou, X. Zhu and QC, ms in preparation), which can be very useful for
charged species. Includes both energy and gradient. Can be used for reaction
path calculations.
Files Added:
source/misc/pbeqscc.src
source/fcm/sccpb.fcm
Files Modified:
build/UNX/misc.mk
source/fcm/pbeq.fcm
source/fcm/sccdftb.fcm
source/energy/energy.src
source/mc/mcener.src
source/misc/gsbp.src
source/misc/pbeq.src
source/misc/pbeq2.src
source/sccdftbint/sccdftbini.src
source/sccdftbint/sccdftbsrc/eglcao.f
source/sccdftbint/sccdftbsrc/shift.f
..............................................................................
3.2.3 DIV scheme for QM/MM boundary
The DIV scheme (JPC-B, 109, 9082-9095 (2005)) is added and bug fix in GSBP
in terms of boundary and reference consistency.
Files Modified:
source/fcm/sccdftb.fcm
source/misc/gsbp.src
source/misc/gsbpscc.src
source/misc/gsbpscc2.src
source/sccdftbint/sccdftbini.src
..............................................................................
3.2.4 SCF convergence criterion added
Added Mulliken-charge based SCF convergence criterion and the option to
print out QM dipole moment. Both are useful for IR spectra calculations based
on classical ACF of QM dipole.
Files Modified:
source/fcm/sccdftb.fcm
source/sccdftbint/sccdftbini.src
source/sccdftbint/sccdftbsrc/eglcao.f
source/sccdftbint/sccdftbsrc/output.f
------------------------------------------------------------------------------
3.3 Constant Pressure Simulation with the Primary Hydration Shell
Developer : Mehdi Bagheri Hamaneh and Matthias Buck
Email Address : matthias.buck@case.edu
Institution : Case Western Reserve University
Date : March 30, 2009
We have modified the primary hydration shell (PHS) method implemented
in the MMFP module. In this method the protein of interest is solvated using
only a thin shell of water, and to prevent evaporation of the solvent,
a half-harmonic force is applied to the water molecules whose distance from
the nearest protein atom is larger than a certain value. The PHS method
greatly reduces the computational cost of molecular dynamics simulations
especially for large systems. In our modified version the method has been
improved in several ways:
1) Despite the fact in PHS simulations the system is non-periodic,
the modified PHS method allows running constant pressure simulations.
This is especially important in the case of the large proteins, because
the external forces applied to the water molecules result in large pressures,
which in turn cause distortion and unfolding of the protein. To reduce
the pressure on the system, a small outward half-harmonic force is applied
to the water molecules that are close to the solvent-vacuum boundary.
By adjusting the ratio of the outward and inward forces the pressure of
the system is held constant at the desired value.
2) The PHS method requires finding the nearest protein atom to each
water molecule. For a large system calculating these distances is very
computationally expensive. We have introduced in a much more efficient
algorithm for distance calculations, which decreases the computational
time several fold.
3) Using the original PHS method usually results in partial desolvation
of some (mostly hydrophobic) parts of the protein. In the modified version of
the method the user may use different force constants for the external forces
applied on the water molecules, depending on the hydrophobicity of the nearest
protein residue. In other words, the force constant for the waters that are
close to non-polar residus may be set to a larger value. This usually results
in a more uniform water distribution around the protein.
Comparisons between the results of simulations with both original and
modified PHS method, and also simulations using the standard methods with
periodic boundary conditions show good agreement between the modified version
and the standard simulations and major improvements over the original method.
For details about the method and also test simulations please see the
following:
M B Hamaneh, and M Buck, Refinement of the primary hydration shell model for
molecular dynamics simulations of large proteins, Journal of Computational
Chemistry, in press.
Files Modified:
doc/mmfp.doc
source/energy/energy.src
source/fcm/mmfp.fcm
source/manip/corman2.src
source/misc/primsh.src
source/pert/epert.src
test/c24test/mmfptest3.inp
------------------------------------------------------------------------------
3.4 Non-Uniform Charge Scaling (NUCS)
Developer : Stefan Fischer
Email Address : stefan.fischer@iwr.uni-heidelberg.de
Institution : University of Heidelberg, Germany
Date : June 24, 2009
The NUCS procedure is a practical approach of implicit solvation
that approximates the solvent screening effect by individually scaling
the partial charges on the explicit atoms of the macromolecule
so as to reproduce electrostatic interaction energies obtained
from an initial Poisson-Boltzmann analysis.
The solvation "Born" self-energy of the partial charges is neglected.
The approach is particularly suitable for minimization-based simulations,
such as normal mode analysis, certain conformational reaction path or
ligand binding techniques for which bulk solvent cannot be included explicitly,
for combined quantum mechanical/molecular mechanical calculations,
when the interface to more elaborate continuum solvent models is lacking.
Details described in
"Non-Uniform Charge Scaling (NUCS): a practical approximation
of solvent electrostatic screening in proteins."
S.M. Schwarzl, D. Huang, J.C. Smith and S. Fischer.
J. Comp. Chem. 26, 1359-1371 (2005).
Files Added:
support/nucs_solvation/nucs_solvation.tar.gz
Modified Documentation:
doc/support.doc
------------------------------------------------------------------------------
3.5 Bugfixes and Enhancements
3.5.1 Prefx key fix
Developer : Stefan Boresch
Email Address : stefan@mdy.univie.ac.at
Institution : University of Vienna
Date : July 1, 2009
Incorrect !##RMD handling in iniall.src
Files involved:
source/charmm/iniall.src
..............................................................................
3.5.2 Variable location fix
Developer : Rick Venable
Email Address : venabler@nhlbi.nih.gov
Institution : LBC/NHLBI/NIH
Date : April 7, 2009
KK is placed out of ##CHEQ block. (dynamc.src) molt_dummy is declared
integer. (psfres.src) qchemp of ##CHEMPERT is placed out of ##PSSP block.
bugfixes on charmm.org
Files involved:
source/dynamc/dynamc.src
source/io/psfres.src
source/fcm/pert.fcm
..............................................................................
3.5.3 DYNA UNFO write fix
Developer : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska Institute
Date : January 27, 2009
With I4BINARY in effect (the default) on a 64-bit system the timestep
written to a binary trajectory created with DYNA UNFO has the value 0.0.
Files involved:
source/dynamc/dynio.src
..............................................................................
3.5.4 DYNAMC with transition path sampling with PNSAve.
Developer : Michael Hagan (via Aaron Dinner)
Email Address : dinner@uchicago.edu
Institution : The University of Chicago
Date : May 13, 2009
Incorrect error handling when setting inconsistent TPS options for
input of a saved trajectory.
Files involved:
source/dynamc/tps.src
..............................................................................
3.5.5 MC with Wang-Landau sampling from an input initial guess
Developer : Aaron Dinner
Email Address : dinner@uchicago.edu
Institution : The University of Chicago
Date : July 23, 2009
Array into which the free energies (middle column of file) are read is
declared as integer rather than real*8 leading to truncation.
Files involved:
source/mc/wl.src
..............................................................................
3.5.6 Routine name corrected
Developer : Thomas Taylor / Stefan Boresch
Email Address : anubis@mdy.univie.ac.at / stefan@mdy.univie.ac.at
Institution : Institut fuer Computergestuetzte Biologische Chemie
Date : 2009-05-28
Compiling with PIPF keyword to enable pipf code does not work out of
the box because of typo. corrected to EPFDRV.
Files involved:
source/nbonds/enbond.src
..............................................................................
3.5.7 VSHIft / RSCAle=0 for some atoms leads to NaN
Developer : Stefan Boresch
Email Address : stefan@mdy.univie.ac.at
Institution : University of Vienna, Austria
Date : June 26, 2009
In free energy simulations with PERT it may be very useful to use
RSCAle to set the LJ interactions of some atoms to zero. We just
noticed by coincidence that this doesn't work with VSHIft (we usually
use VSWItch). Since any fix (suggestions below) touches the inner loop
of the (slow) energy routines (EVDW in enbonda.src), I'd appreciate
feedback before submitting a formal bugfix. Consider the following
fragment from enbonda.src (ca. line 804ff in c36a2):
IF (S.LT.C2OFNB) THEN
SGSHSQ=RSCLF(I)*RSCLF(J)*CNBA(IC)
SIG2=SGSHSQ*R2
SIG6=SIG2*SIG2*SIG2
SIG12=SIG6*SIG6
SGSHSQ=SGSHSQ*RECOF2
SGSHSQ=SGSHSQ*SGSHSQ*SGSHSQ
ASH6=TWO*(SGSHSQ-ONE)*SGSHSQ*SGSHSQ/SIG6 ! <----
BSH6=(THREE*SGSHSQ-FOUR)*SGSHSQ
C
ENBPR=(CNBB(IC)*(SIG12-SIG6-SIG6+ASH6-BSH6))
DF=CNBB(IC)*R2*(TWELVE*(SIG6-SIG12)+SIX*ASH6)
As you can see, SGSHSQ becomes zero if RSCLF of either atom
I or J is zero, leading to a division by zero in the line
marked by <----
Realizing that SGSHSQ/SIG6 equals (RECOF2/R2)**3 leads to
an obvious fix of the offending line
Avoid the 0/0 expression by rewriting the offending line as
ASH6=TWO*(SGSHSQ-ONE)*SGSHSQ*(RECOF2/R2)**3
Files involved:
source/nbonds/enbonda.src
..............................................................................
3.5.8 cstuff.c fix
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 : July 4, 2009
pointers fixed in funtion uninf.
Files involved:
source/machdep/cstuff.c
------------------------------------------------------------------------------
3.6 Carbohydrate force field
Developer : Alex MacKerell, Olgun Guvench, Liz Hatcher
Email Address : alex@outerbanks.umaryland.edu
Institution : Univ. of Maryland, School of Pharmacy
Date : August 9, 2009
New versions, deemed all36, of the carbohydrate RTF and PRM files
containing fully optimized parameters for the acyclic sugars, the glycosyl
linkages in hexopyranoses and the furanose monosaccharides.
Files Removed:
toppar/par_all35_carb.prm
toppar/top_all35_carb.rtf
Files Added:
toppar/par_all36_carb.prm
toppar/top_all36_carb.rtf
