ChangeLog.c32
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CHARMM 32 |
| c32a1 |
Developmental |
August 15, 2004 |
| c32a2 |
Developmental |
February 15, 2005 |
| c32b1 |
Release |
August 15, 2005 |
| c32b2 |
Release |
February 15, 2006 |
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|
About CHARMM32 Development |
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At the July 2004 CHARMM meeting (Harvard University, July 9-10, 2004),
we decided to release CHARMM c31b1 with incorporating enhancements and fixes
to the developmental version c31a2. The modified source code and features
are described in ChangeLog.c31, [4] c31b1 Change Log.
As an on-going project, CHARMM development will be carried out
with CHARMM version 32a series. The following describes new features
and enhancements incorporated in the c32 development period.
The following are introduced and modified during the development period
of February 15, 2004 through August 15, 2004. The developments are
based on CHARMM version c31a2. Some enhancements and fixes to c31a2
are also incorporated into c31b1 as described in the c31b1 release note
(ChangeLog.c31).
1.1 University of Wisconsin Developments
Developers : Patti Schaefer, Mark Formaneck and Qiang Cui
Email Address : cui@chem.wisc.edu, psschaefer@wiscmail.wisc.edu
formanec@chem.wisc.edu
Institution : University of Wisconsin, Madison
Date : July 1, 2004
1.1.1 GSBP and eWald Sum Codes added to the SCC-DFTB/MM Framework
The generalized solvent boundary potential (GSBP) originally developed
by Roux and co-workers for MM simulations, has been combined with the
SCC-DFTB/MM code. In addition, eWald summation has been integrated with
SCC-DFTB/MM. These developments can be extended in straightforward manners
to other QM codes, although the implementation is somewhat easier for
SCC-DFTB due to its specific representation of charge density.
Files Added:
source/fcm/sccgsbp.fcm
source/misc/gsbpscc.src
source/sccdftbint/sccdftbsrc/ktable_ewscc.f (Setting up kspace table)
source/sccdftbint/sccdftbsrc/long_sccmm1.f (Different ways of getting
source/sccdftbint/sccdftbsrc/long_sccmm2.f the eWald potential)
Files Removed:
source/sccdftbint/sccdftbsrc/xnorm.f
source/sccdftbint/sccdftbsrc/vnorm.f
Files Modified:
build/UNX/sccdftb.mk (removed xnorm,vnorm; added long_sccmm1/2; ktab*)
source/energy/energy.src (GSBP/Mulliken)
source/fcm/sccdftb.fcm (added Mulliken, ewald)
source/fcm/blockscc.fcm (Cleaned up)
source/fcm/pbeq.fcm (GSBP exclusion for QM/MM)
source/misc/gsbp.src (GSBP)
source/misc/pbeq.src (related to GSBP)
source/nbonds/nbonds.src (remove warning about eWald)
source/sccdftbint/sccdftbsrc/dylcao.f (ewald)
source/sccdftbint/sccdftbsrc/eglcao.f (GSBP)
source/sccdftbint/sccdftbsrc/external*f (ewald)
source/sccdftbint/sccdftbsrc/gamma.f (charge-Hubbard)
source/sccdftbint/sccdftbsrc/gammamat.f (ewald)
source/sccdftbint/sccdftbsrc/long_range.f (ewald)
source/sccdftbint/sccdftbsrc/mulliken.f (added Mulliken transfer)
source/sccdftbint/sccdftbsrc/shift.f (GSBP and charge-Hubbard)
source/sccdftbint/sccdftbini.src (ewald/Mulliken/Hubbard
enforce FAST OFF for DTSC-FEP)
Modified Documentation:
sccdftb.doc
New Testcases:
c32test/scc_fep_dtsc.inp (DTSC-FEP calculations for redox potential)
data/top_qc27.inp
data/par_qc27.inp (include FAD)
data/chox_sb_scal_q.psf
data/chox_minimized.crd
data/chox_sb_q.cns
data/chox_sb_q-min.crd
data/chox_st_equ_one.res
c32test/scc_pka1.inp
c32test/scc_pka2.inp (DTSC-FEP pKa calculations for EtSH)
data/etsh.psf,etsh-min.crd
data/etsh-pka1-equ-0.70.res
data/etsh-pka2-equ-0.95.res
c32test/scc_ewald_triala.inp (eWald calculation with SCC-DFTB/MM
for solvated tri-alanine)
data/triala_solv.psf
data/triala_solv.crd
c32test/sccgsbp1_2cba.inp (examples for setting up an enzyme
c32test/sccgsbp2_2cba.inp - carbonic anhydrase - calculation
c32test/sccgsbp3_2cba.inp using SCC-GSBP)
c32test/sccgsbp4_2cba.inp
data/top_ca.inp (included Zinc related RTF)
data/par_ca.inp
data/2cba.psf (solvated carbonic anhydrase)
data/2cba.crd
Note: making sccdftb.a automatically added to the Makefile by
install.com requires adding "sccdfbint.a" into the default object
list in build/UNX/Makefile*
..............................................................................
1.1.2 BNM and DTSC Codes Cleaned
Codes for block normal mode analysis (BNM) and the dual-topology-
single-coordinate(DTSC) SCC-DFTB/MM FEP calculations (including pKa)
have been cleaned up.
Files Modified:
source/vibran/vibran.src (adopted patch)
source/energy/eintern.src (adopted VIBRAN---> VIBPARA; fix for DTSC-FEP)
source/energy/energy.src
source/dynamc/dcntrl.src (fix for DTSC-FEP)
source/dynamc/dynamc.src
source/dynamc/dynamc4.src
source/dynamc/dynamcv.src
source/dynamc/dynamvv.src
source/dynamc/dynio.src
source/misc/eef1.src (adopted VIBRAN---> VIBPARA)
source/nbonds/enbond.src
source/nbonds/nbonda.src
source/nbonds/nbondg.src
source/nbonds/nbonds.src
source/nbonds/enbonda.src (fix for DTSC-FEP)
Modified Documentation:
vibran.doc
Modified Testcase:
bnmtest.inp (modified BNM input)
..............................................................................
1.1.3 New CONS RMSD Functional Form
Added the Zeta functional form to the Relative RMSD restraint.
Also added two atoms selection - atoms in first selection are affected
by the restraint, atoms in the second selection are used in fitting the
reference structures. In order to utilize these two selections, the
fitting and restraint application routines were separated (before, this
was done in the same routine) and the arrays were reworked. This will
cause some extra work for using the code in the manner that was
originally coded for, but the results are the same. Also,
we added functionality to call the fitting routine every INRT steps,
which can help to save on calculation time.
Files Modified:
source/energy/ecnstr.src (addition of extra HEAP space, used in ECNST3)
source/energy/rmsd.src (Major Changes, Added Subroutines)
source/fcm/rmsd.fcm (added variables)
source/manip/cstran.src (added selection array, KSLCT, used in SETRMSD0)
Modified Documentation:
doc/cons.doc
New Testcase:
c32test/cons_rmsd_zeta.inp
data/cons_rmsd_zeta.psf
data/cons_rmsd_zeta-ref1.crd
data/cons_rmsd_zeta-ref2.crd
..............................................................................
1.1.4 New TMD Functional Form
Added capability to use two different target structures with TMD, using
the Zeta form of the constraint only. Now, two selections can be used
for either form (original or new) of the TMD constraint -
first selection is for fitting targets, second selection is for applying
the TMD constraint. One selection defines both functionalities for the
same selection. Most of the code for the original, one-target TMD has been
untouched, and extra subroutines were created for the Zeta form. Also,
added a call to fit the targets to the current structure upon calling
dynamics, instead of waiting until step=INRT, as first implemented. This
new code is not parallelized.
Files Modified:
source/dynamc/dcntrl.src (Major Changes, added Zeta terms)
source/dynamc/dynamc4.src (minor 'call wridyn' changes)
source/dynamc/dynamc.src (Major Changes, added Zeta terms)
source/dynamc/dynio (readyn and wridyn uses more variables for Zeta form,
and a second target structure is saved in
restart file)
source/dynamc/tmd.src (Major Changes, Added Subroutines)
source/fcm/tmd.fcm (added variables)
source/io/coorio.src (minor 'call readyn' changes)
source/io/mainio.src (now can read and write 2nd target structure)
source/mbond/mbback.src (minor 'call wridyn' changes)
source/mc/mcio.src (minor 'call readyn/wridyn' changes)
source/mc/mvhmc.src (minor 'call dynamc' changes)
Modified Documentation:
doc/dynamc.doc
New Testcase:
c32test/tmd_zeta.inp
------------------------------------------------------------------------------
1.2 TSRI Developments
Developers : Scott Brozell, Mike Crowley, Charles L. Brooks, III
Roberto GOmpers (SGI)
Email Address : sbrozell@scripps.edu, crowley@sripps.edu,
brooks@scripps.edu
Institution : The Scripps Research Institute
Date : July 4, 2004
1.2.1 4-Byte Integer Binary IO
64 bit integers are default for many architectures now.
Trajectories and other binary files written by charmm are unreadable
on other machines when the binary files contain 64 bit integers.
This mod makes all binary io restricted to 32 bit integers only
Files Modified:
install.com
source/correl/solana.src
/dimb/dimbsub.src
/dynamc/dynio.src
/dynsub.src
/fcm/iochan.fcm
/deflts.fcm
/gener/hbonds.src
/image/xtlfrq.src
/io/coorio.src
/parmio.src
/psfres.src
/machdep/cstuff.c
/machio.src
/manip/corman2.src
/intcor.src
/molvib/molvio.src
/nbonds/etable.src
/util/datstr.src
/title.src
/util.src
/vibran/rbquas.src
/redbas.src
vibio.src
Modified Testcase:
c31test/endian.inp
..............................................................................
1.2.2 Performance Enhancement of ENBFS8
Loop rearrangement and temporary arrays for locality to speed up
fast nonbond routine.
Files Added:
source/fcm/enbfs8p.fcm
source/nbonds/enbfs8p.src
Files Modified:
install.com
source/nbonds/enbfast.src
/util/new_timer.src
..............................................................................
1.2.3 64 bit Parallel and Serial IBMAIX Codes
Files Added:
build/UNX/Makefile_ibmaix
/Makefile_ibmaix64
/Makefile_ibmaixmp64
Files Modified:
install.com
source/correl/solana.src
/machdep/cstuff.c
/paral1.src
/paral2.src
/space.src
/manip/shake.src
/nbonds/pmeutil.src
------------------------------------------------------------------------------
1.3 Developments at the National Institute of Health
Developers : H. Lee Woodcock, Xiongwu Wu and Bernard R. Brooks
Email Address : hlwood@nih.gov, wuxw@nhlbi.nih.gov, brb@nih.gov
Institution : Laboratory of Biophysical Chemistry, NHLBI, NIH
Date : July 1, 2004
1.3.1 New Monte Carlo-minimization/annealing (MCMA) method
A Monte Carlo-minimization/annealing (MCMA) routines for
biased sampling of polypeptide conformations and for
docking simulations has been added. This method is based
on the IC tables in CHARMM and been demonstrated to work
very well in determining low energy conformation of proteins.
1. Moves for peptide/protein structure prediction:
bias, back, main, side, all
2. Moves for docking one molecule (segid SEGMOV, resid RESMOV):
rota, tran, rotr
Acceptance of docking moves: accm, accr, acct, accb
or rotated (or both) each step.
Random changes are made to PHI, PSI, COS(THETA) and
X, Y, Z. PHI, PSI, and THETA are the Euler angles
specifying the current orientation of the ligand relative
to the previously accepted orientation.
References: PJ Steinbach, Proteins 2004, in press.
Abagyan & Totrov, JMB 1994.
Li and Scheraga, PNAS 1987.
Files Added:
source/fcm/mcma.fcm
source/mc/mcma.src
File Modified:
source/charmm/charmm_main.src
..............................................................................
1.3.2 Autogenerate for Patching Option
An autogenerate feature has been added to the RTF reader and the
PATCh command which allow the autogeneration of angles and dihedrals.
The PATCH command syntax:
PATCh misc-patch-spec residue-list-spec
misc-patch-spec ::= [SORT] [SETUp] [WARN] [ ANGLe ] [ DIHEdrals ]
[ NOANgle ] [ NODIhedral]
The RTF reader AUTOgenerate command syntax:
AUTOgenerate [ ANGLes ] [ DIHEdrals ] [ PATChes ] [ NONE ]
[NOANgles] [NODIhedrals] [NOPAtches]
Note that autogenerate is not the default and must be requested.
The specifications in the PATCH command override the specification
in the RTF.
Files Modified:
source/charmm/iniall.src
source/fcm/rtf.fcm
source/gener/genpsf.src
source/gener/modpsf.src
source/io/rtfio.src
..............................................................................
1.3.3 New MANTIM STATe and HEAViside Functions
CORRECL has two new operations, STATe and HEAViside.
MANTIME name { STATe minv maxv } ! Q(t) = 1 (minv < Q(t) < maxv), else = 0
{ HEAViside } ! Q(t) = 0 (when Q(t)<0), else = 1
Files Modified:
source/correl/correl.src
source/correl/mantim.src
..............................................................................
1.3.4 New Crystal type "RECTangular"
A new crystal type "RECTangle" has been added to the CRYStal DEFIne
command. This new type is the same as "ORTHorhombic", except that the
ratios of the unit cell dimensions are fixed. The total volume may change.
RECTangular - a/A = b/B = c/C and alpha = beta = gamma = 90.0 degrees.
(Note: A,B,C are the initial a,b,c values)
(example: 50.0 40.0 30.0 90.0 90.0 90.0 )
(volume = c*b*a)
(degrees of freedom = 1)
The undocumented ISOTropic option in the DYNAmics command has been removed,
since it never worked properly and the new code make its intended
function obsolete.
Files Modified:
source/dynamc/dynamvv2.src
source/dynamc/prssre.src
source/energy/energy.src
source/fcm/image.fcm
source/image/crystal.src
source/image/eimage.src
source/image/xtlfrq.src
source/mc/mcener.src
source/mc/mcmini.src
source/minmiz/abner.src
source/minmiz/conjug.src
source/minmiz/egrad1.src
source/minmiz/nraph.src
source/minmiz/powell.src
source/minmiz/steepd.src
source/minmiz/tndriv.src
source/misc/testch.src
source/pert/epert.src
..............................................................................
1.3.5 Isotrop Periodic Sum Code (IPS)
A new isotropic periodic sum method has been developed. This
code is intended as a reasonable alternative to Ewald and vdw LRC
correction methods. The new code has been developed for 3-D, 2-D
and 1-D periodic systems. There are lots of new options, but the
main nonbond keywords are [EIPS] [VIPS] [RIPS real].
See nbonds.doc for details.
Files Added:
source/fcm/nbips.fcm
source/nbonds/enbips.src
test/c31test/ips_tip216.inp
Files Modified:
doc/nbonds.doc
source/energy/energy.src
source/fcm/inbnd.fcm
source/image/nbondm.src
source/nbonds/enbfast.src
source/nbonds/enbond.src
source/nbonds/enbonda.src
source/nbonds/enbondg.src
source/nbonds/nbonda.src
source/nbonds/nbondg.src
source/nbonds/nbonds.src
source/nbonds/nbutil.src
..............................................................................
1.3.6 Add SCALAR WRITE Command
There is a new SCALar WRITe command to output data arrays in CHARMM.
File Modified:
source/manip/scalar.src
..............................................................................
1.3.7 New Expanded Fast Routines and Fast Control
A new set of FAST routines have been developed. These have been
written as a single routine that becomes expanded into many
"cleaned" routines that are free of unnecessary code (e.g. IF tests).
Use of these routines will significantly improve performance.
FAST OFF ! Use the slow full-feature routines
FAST GENEric ! Use the old "fast" routines (that are no longer fast)
FAST ON ! Use best routine available for current calculation
FAST EXPAnd ! Use new expanded routines
Files Added:
source/nbonds/enbaexp.src
source/nbonds/enbgexp.src
Files Modified:
source/charmm/miscom.src
source/energy/enefscal.src
source/energy/energy.src
source/energy/intere.src
source/fcm/fast.fcm
source/image/eimage.src
source/mbond/mbdiag.src
source/mc/mcimge.src
source/misc/genetic.src
source/nbonds/enbond.src
source/pert/epert.src
source/pert/icfcnf.src
source/pert/icpert.src
source/pert/tsme.src
source/vibran/vibblock.src
..............................................................................
1.3.8 Inline ERFC Code for Faster Ewald
The ERFC lookup table code has been simplified (fewer operations)
and now works with a zero distance (good for DRUDE), which eliminated
a pair of inner loop IF tests.
Files Modified:
source/cff/ewald_cff.src
source/fcm/ewald.fcm
source/mmff/enbscalar_mm.src
source/nbonds/ewald.src
source/nbonds/nbutil.src
..............................................................................
1.3.9 Improve the PRESsure INSTantaneous Command.
The PRESsure INSTantaneous command now works with a zero temperature.
Additional virial and pressure data is printed.
Files Modified:
source/dynamc/prssre.src
..............................................................................
1.3.10 NUMLP
Set ?NUMLP variable for the number of lonepairs.
Files Modified:
source/dynamc/lonepair.src
source/gener/psfsum.src
..............................................................................
1.3.11 PRNLEV Control
Change PRNLEV values to improve print control.
Files Modified:
source/energy/printe.src
source/image/images.src
source/nbonds/heurist.src
source/nbonds/nbonds.src
..............................................................................
1.3.12 Energy Call Control
To facilitate routine selection in ENBOND, a universal flag, QGCMC,
has been added. (Aaron, would you check on this? mctest02.inp seems to
generate energy blow-out. I fixed part of it, yet does not work correct.)
Files Modified:
source/charmm/iniall.src
source/fcm/gcmc.fcm
..............................................................................
1.3.13 Move ACE Code
The ACE common block code was added to a structured data file in
fcm/inbnd.fcm (which violates the rules governing structured data
files). It also inhibited further development of inbnd.fcm.
The ACE arrays have been moved to the file fcm/ace.fcm.
File Added:
source/fcm/ace.fcm
Files Modified:
source/charmm/iniall.src
source/dynamc/dcntrl.src
source/fcm/inbnd.fcm
source/io/mainio.src
source/manip/cstran.src
source/manip/scalar.src
source/mc/mc.src
source/mc/mcace.src
source/mc/mcener.src
source/nbonds/ace.src
source/nbonds/nbonds.src
source/nbonds/nbutil.src
source/util/selcta.src
..............................................................................
1.3.14 Set KBT and expand format statement
The variable KBT was not properly set.
File Modified:
source/dynamc/dcntrl.src
..............................................................................
1.3.15 Optional Exit for SHAKE Error
Added an optional exit for SHAKE tolerance exceeded errors.
By setting BOMLEV to 1 or more, you can make CHARMM die on this error.
File Modified:
source/manip/shake.src
..............................................................................
1.3.16 Fix bugs/problems with ##IF usage
There were a number of ##IF control problems. The use of the inline
precompile selection: !##IF CHEQ
is wrong. The correct syntax is !##CHEQ
Also, spaces within ## line identifiers is not allowed.
Files Modified:
source/fcm/param.fcm
source/fcm/traj.fcm
source/fcm/vibblock.fcm
source/image/upimag.src
source/vibran/vibran.src
..............................................................................
1.3.17 Fix QECONT and ATOMON Bugs
The use of QECONT and filling the ECONT array was wrong.
File Modified:
source/misc/eef1.src
..............................................................................
1.3.18 Fix SCALAR READ Parallel Bug
There was a bug in the SCALar READ command when used in a parallel
calculation. This has been fixed.
File Modified:
source/manip/scalar.src
..............................................................................
1.3.19 Fix Compile and Timer Bugs in SPAS Code
The SPAS code would not compile properly. It still does not work
and it consumes massive quantities of memory... The code should
be reworked or removed.
Files Modified:
source/energy/energy.src
source/io/parmio.src
..............................................................................
1.3.20 NUMBERs and CONSTANTs
The use of real*8 numbers in calling sequences has been corrected.
This is non-standard and causes problems on some compilers.
Also, I made an effort to make the use of constants more consistent.
For example, I replaced instances of 332.0... with the parameter CCELEC
in fcm/consta.fcm.
Files Modified:
source/dynamc/dynamcv.src
source/dynamc/dynamln.src
source/dynamc/dynamvv.src
source/dynamc/dynamvv2.src
source/energy/ecmap.src
source/energy/gbmv.src
source/energy/gbsw.src
source/fcm/consta.fcm
source/io/coorio.src
source/io/rtfio.src
source/mbond/mbback.src
source/mc/mcio.src
source/misc/genetic2.src
source/nbonds/pmeutil.src
source/util/random.src
..............................................................................
1.3.21 Fix Spelling
File Modified:
source/fcm/rndnum.fcm
..............................................................................
1.3.22 QM/MM Interface Using the Q-Chem Quantum Chemistry Package
Added a QM/MM interface to Q-Chem using the GAMESS-US and GAMESS-UK
interface as a model. Q-Chem and CHARMM communicate via files rather than
common blocks which means the two programs live separately.
The Q-Chem QM/MM interface was also extended to function with the
highly parallel Replica/Path and the Nudged Elastic Band Methods.
Files Modified:
install.com
source/charmm/charmm_main.src
source/charmm/iniall.src
source/energy/energy.src
source/fcm/gamess.fcm
source/fcm/replica.fcm
source/fcm/path.fcm
source/gener/update.src
source/gukint/gukini.src
source/nbonds/nbonda.src
source/nbonds/nbonds.src
source/quantum/addlnat.src
..............................................................................
1.3.23 Q-Chem Input Generation
Added the ability of zmat.src to write out Q-Chem input files. This
occurs in the same way that the Gausssian interface is used.
File Modified:
source/misc/zmat.src
..............................................................................
1.3.24 Off-Path Optimization and Simulation
The new EPATHO procedure was added which allows a user to run
orthogonal simulations at each replica/bead/point along a replica or
NEB path. These simulations are used to compute the free energy of
reaction.
Curvature corrections to these simulations were also added, but have
not been throughly tested to determine their usefulness.
Files Modified:
source/energy/epath.src
source/fcm/path.fcm
source/fcm/replica.fcm
source/fcm/gamess.fcm
------------------------------------------------------------------------------
1.4 Developments at NIC-Slovenia
Names : Milan Hodoscek
Email Address : milan@cmm.ki.si
Institution : National Institutes of Chemistry, Ljubljana, Slovenia
Date : June 30, 2004
1.4.1 New version of GAMESS supported
New version of GAMESS (19 May 2004 (R3)) is interfaced with
CHARMM. New features include Fragment MO, NMR shifts, improved
DFT convergence and many others.
Files Modified:
doc/gamess.doc
source/fcm/gamess.fcm
source/flucq/fluqqmmm.src
source/gamint/blur.src
source/gamint/ddi.src
source/gukint/gukini.src
source/gamint/gamess/{grd2a.src,int1.src,mccas.src,prplib.src,
prppop.src,prpel.src,unport.src,zunix.c,
gamess.src,grd1.src,guess.src,inputb.src,
inputc.src,iolib.src,scflib.src,rhfuhf.src,
inputa.src}
..............................................................................
1.4.2 Parallelization of DRUDE, LONEPAIR and VV2 integrator
DRUDE and VV2 integrator are parallelized. For efficiency also
LONEPAIR had to be parallelized.
Files Modified:
source/gener/drude.src
source/manip/holonom.src
source/machdep/paral1.src
source/energy/ediff.src
source/energy/energy.src
source/dynamc/lonepair.src
source/dynamc/dcntrl.src
source/dynamc/dynamvv2.src
source/dynamc/dynamcv.src
source/dynamc/dynamc.src
source/dynamc/dynio.src
source/nbonds/nbonds.src
..............................................................................
1.4.3 Parallelization of SSBP and GSBP
Spherical Solvent Boundary Potential method was parallelized.
General Solvent Boundary Potential method parallelization started.
Currently works in parallel environment, but not parallelized yet.
Files Modified:
doc/parallel.doc
source/energy/energy.src
source/misc/ssbp.src
source/misc/gsbp.src
source/misc/pbeq2.src
..............................................................................
1.4.4 Enhancements for GRAPE interface
Several enhancement in the GRAPE interface.
Files Modified:
source/nbonds/grape.src
..............................................................................
1.4.5 Fix and extension of SOLANA
The calculation of rotational correlation in SOLANA was wrong.
It is fixed and extended to use Legendre polynomials of second order,
by introducing new command keyword RLP .
Files Modified:
doc/corman.doc
source/charmm/iniall.src
source/correl/solana.src
source/fcm/corman.fcm
..............................................................................
1.4.6 Parallelization of RANDOM code and fix for NEWRNG
Parallelization of standard RANDOM number generator. Also the
usage of CLCG generator was fixed at the same time.
Files Modified:
source/charmm/iniall.src
source/correl/solana.src
source/dynamc/dcntrl.src
source/dynamc/dynamc.src
source/energy/gbmv.src
source/fcm/clcg.fcm
source/fcm/parallel.fcm
source/manip/intcor.src
source/mc/mc.src
source/misc/genetic.src
source/misc/pbeq.src
source/util/clcg.src
source/util/random.src
source/vibran/vibran.src
..............................................................................
1.4.7 Fixes for various ## keywords
Some of the ## keywords would not allow compilation of CHARMM if
excluded from pref.dat. New set of fixes for this are in:
Files Modified:
source/energy/eintern.src
source/energy/energy.src
source/nbonds/enbfast.src
source/nbonds/nbonds.src
source/mc/mcener.src
------------------------------------------------------------------------------
1.5 Harvard Developments
Name : Arjan van der Vaart, Robert Petrella
Email Address : arjan@tammy.harvard.edu, petrella@tammy.harvard.edu
Institution : Harvard University
Date : June 29, 2004
1.5.1 Revision of TMD.
Enhancement and streamlining of the TMD code. Introduced the
"FRMS" keyword, that causes TMD dynamics to stop when a user defined
rmsd has been reached. Introduced a selection statement for TMD, that
allows application of TMD to a subset of atoms. Removed all TMD statements
in the DYNA command: all TMD commands are now parsed in the TMDInitialize
command. Removed the NTAR and TARGET keywords since these are redundant.
Removed writing of TMD info to restart files, and TMD memory is now
deallocated upon finish of DYNA command.
Files Modified:
source/charmm/charmm_main.src
source/dynamc/dcntrl.src
source/dynamc/dynamc4.src
source/dynamc/dynamc.src
source/dynamc/dynio.src
source/dynamc/tmd.src
source/energy/eutil.src
source/fcm/tmd.fcm
source/io/coorio.src
source/io/mainio.src
source/mbond/mbback.src
source/mc/mcio.src
source/mc/mvhmc.src
source/minmiz/minmiz.src
New Documentation:
doc/tmd.doc
Modified Documentation:
doc/dynamc.doc
doc/io.doc
Modified Testcase:
test/c31test/tmdtest32.inp
..............................................................................
1.5.2 BYCC Enhancements
1) SUBROUTINE NBNDCC made into two routines:
NBNDCCF --for fastest execution, stripped of options
NBNDCCO --for compatibility with various options.
The latter routine is the one where developers should add functionality
to BYCC.
2) BYCC made compatible with heuristic updates
(for both atom-based and group-based calculations)
3) Changes in logic for calling cluster-generating routine
(SUBROUTINE CLSBYRULE).
A) Clusters are made by default prior to updating
the list if "BYCC" is specified in the update command
(unless they have previously been made).
B) An informed guess is made as to whether the connectivity
or the topology of the system has changed before calling
NBNDCC. If a change is detected, the clusters are
remade prior to non-bonded list generation. This is
done because changes in the connectivity may necessitate
the formation of new clusters, and significant changes in the
topology almost certainly do.
(changed subroutine: GTNBCT)
4) added global bycc QLBYCC in actclus.fcm to indicate BYCC
has been specified in non-bonded command (for use in other
parts of charmm).
5) minor modifications in eef1 code for compatibility with BYCC
6) BYCC made compatible with TSM
7) clustering algorithm made faster (now clusters
roughly 1,000,000 atoms/s on 2.66 GHz Pentium 4)
Files Modified:
source/charmm/iniall.src
source/nbonds/nbndcc.src
source/nbonds/nbonds.src
source/nbonds/nbutil.src
source/misc/eef1.src
source/fcm/actclus.fcm
------------------------------------------------------------------------------
1.6 Developments at University of Vienna
Developers : Tibor Rudas, Stefan Boresch and Othmar Steinhauser
Email Address : tibi@mdy.univie.ac.at and stefan@mdy.univie.ac.at
Institution : Molecular Dynamics and Biomolecular Simulation group
at the Department of Theoretical Chemistry and
Molecular Structural Biology, University of Vienna
Date : June 23, 2004
1.6.1 COM Centering in COOR DIPO
When calculating the dipole moment of a set of atoms carrying a total
net charge the coordinates of this set are recentered to the center of
geometry of these atoms. Adding a MASS keyword to the invocation (which
is present for many other COOR commands) allows the center of mass as
locus of recentering.
Both this keyword and the recently introduced OXYZ keyword (which
avoids this recentering unsing the absolute coordinates) are also
introduced into the DIPO series of CORREL.
All calls to CDIPOLE are updated but where no use/parsing of a MASS
keyword is provided/necessary .FALSE. and 0 are passed instead of MASS
and AMASS (solana.src)
Files Modified:
source/correl/correl.src
source/correl/anacor.src
source/correl/solana.src
source/manip/corman.src
Modified Documentation:
doc/corman.doc
doc/correl.doc
..............................................................................
1.6.2 SHELLs of Different Thickness
Instead of the (still supported) keyword SHTH which defines a single
thickness used for all shells generated shells of different thickness
can be defined by using the new SHBO keyword.
Following this keyword should be NSHL real numbers which represent the
boundaries between the single shells (so these numbers should all be in
increasing order).
Files Modified:
source/fcm/shell.fcm
source/correl/shell.src
source/charmm/iniall.src
Modified Documentation:
doc/shell.doc
Modified Testcase:
test/c31testshell.inp
------------------------------------------------------------------------------
1.7 Karolinska Institute Fixes and Enhancements
Developer : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska Institute
Date : July 1, 2004
1) Added possibility to compute water-dipole rotational correlation fcn (P1
or P2), also works in shell defined by RSPIN & RSPOUT
Files Modified:
source/correl/solana.src
doc/corman.doc
test/c27test/solanal2.doc (seemed unnecessary to add another file for this)
2) Set CHARMM variable CFNORM to the normalization used in CORREL CORFUN,
and added possibility to supply the normalization value to be used by
CORFUN; useful to get correctly normalized partial correlation fcns.
Files Modified:
source/correl/solana.src
source/correl/correl.src
source/correl/corfun.src
doc/correl.doc
doc/subst.doc
3) Added substitution variables CPUTIME and ELATIME
Files Modified:
source/machdep/machutil.src
doc/subst.doc
4) Corrected documentation of defaults for CORREL CORR (Legendre pol. P0 is
a constant..)
File Modified:
doc/correl.doc
------------------------------------------------------------------------------
1.8 Implicit Membrane Model 1 (IMM1) and EEF1 update
Developer : Themis Lazaridis
Email Address : tlazaridis@ccny.cuny.edu
Institution : City College of New York/CUNY
Date : May 17, 2004
IMM1 is an extension of the EEF1 implicit solvation model to lipid
membranes. The membrane hydrocarbon interior is modeled as cyclohexane,
with a smooth, monotonic transition between the interior and the aqueous
region.
Electrostatic screening is modeled using a modified distance-dependent
dielectric function (eps=r**l, where l depends on the position of the
two atoms with respect to the membrane.
In addition, updated parameters for EEF1 are provided (referred
to as EEF1.1) and also a version of EEF1 based on CHARMM22.
Files Added:
support/aspara/toph19_eef1.1.inp
support/aspara/param19_eef1.1.inp
support/aspara/top_all22_prot_eef1.inp
support/aspara/top_all22_prot_eef1.1.inp
support/aspara/solvpar22.inp
Files Modified:
source/fcm/eef1.fcm
source/energy/energy.src
source/energy/intere.src
source/misc/eef1.src
source/nbonds/enbfast.src
support/aspara/solvpar.inp
Modified Documentation:
doc/eef1.doc
------------------------------------------------------------------------------
1.9 Multiple Gaussian Job Input Generation
Developers : Victor Anisimov and Alex D. MacKerell, Jr.
Email Address : victor@outerbanks.umaryland.edu
Institution : University of Maryland
Date : June 28, 2004
Gaussian program uses "--link1--" string to separate multiple jobs.
On the other hand hyphen symbol is treated by CHARMM as line continuation
instruction. As a result, CHARMM was merging the "--link1--" string,
which is a Gaussian instruction, with the next line. A correction has
been made to instruct the CHARMM command line reader to turn off the line
continuation mechanism for the moment of Gaussian file generation.
The command line parser ignores hyphen symbol when the parser is
invoked from G94INP routine. Logical variable USEHYP is introduced
for this purpose. USEHYP set to .TRUE. enables line continuation
mechanism (CHARMM default). USEHYP set to .FALSE. disables line
continuation (call from G94INP routine).
File Modified:
source/util/parse.src
------------------------------------------------------------------------------
1.10 Grand Canonical Monte Carlo Enhancements
Developers : Aaron R. Dinner, Hyung-June Woo and Benoit Roux
Email Address : dinner@uchicago.edu
Institution : The University of Chicago
Date : July 19, 2004
The grand canonical Monte Carlo (GCMC) code was substantially enhanced,
essentially completing its implementation for molecular liquids like
water in the presence of protein solutes. In particular, the following
was done:
1. Orientation bias for insertion was added.
2. The grid update is now exact, rather than approximate, allowing
grand canonical simulations involving the movement of arbitrarily
large rigid bodies (e.g., protein side chains). Memory usage was
also improved.
3. Support for the GSBP energy term was added. However, the full term
is calculated at each MC step, making it computationally costly.
4. Various minor deficiencies in the initial implementation were corrected.
Files Modified:
doc/mc.doc
source/mc/mc.src
source/mc/mcener.src
source/mc/mcio.src
source/mc/mvgcmc.src
source/mc/mvrtrn.src
source/fcm/gcmc.fcm
source/fcm/pbeq.fcm
source/manip/scalar.src
source/misc/gsbp.src
source/misc/pbeq2.src
------------------------------------------------------------------------------
1.11 University of Minnesota Developments
Developers : Jingzhi Pu, Jiali Gao, and Donald G. Truhlar
Email Address : pu@comp.chem.umn.edu
Institution : University of Minnesota
Date : July 2004
1.11.1 GHO Boundary Treatment for SCC-DFTB/MM
The generalized hybrid orbital (GHO) method is implemented for
the self-consistent-charge density-functional tight-binding
(SCC-DFTB) theory and molecular mechanics (GHO-SCC-DFTB/MM). A full
description of the algorithm is given in J. Phys. Chem. A 2004, 108,
5454. Several issues regarding the implementation are discussed
below:
The current GHO implementation for SCC-DFTB largely resembles the one
for the semiempirical QM module in CHARMM. Therefore, a large majority
of the data structure and basis transformation routines are the same and used.
The new file source/fcm/stbgho.fcm has a large part of overlap with
source/fcm/qmlink.fcm. Similarly, the new file source/sccdftbint/stbgho.src
also contains some subroutines that have already been included in
source/quantum/qmset.src. However, the multiple occurrence of these codes
will not conflict with each other, because they are subjected to the
conditional compilation options. Since the QUANTUM and the SCCDFTB module
are mutually exclusive, only one set of these subroutines or common block
data will be actually compiled.
In GHO-SCC-DFTB, the torsion across the QM/MM boundary is treated
somewhat differently than the case where a link atom is used. If we denote
the GHO boundary atom as B and denote the QM atom bonded to the GHO boundary
atom as A, the MM energy for X-A-B-X type torsions will be included in the
total energy. For a link atom treatment, such MM torsions would be excluded
from the total energy since both the central atoms are QM atoms. We prefer
to retain the X-A-B-X torsions in the GHO method to obtain a more realistic
rotational energy profile. The corresponding modification has been made in
the file source/gener/update.src.
Files Added:
doc/sccdftb.doc
source/sccdftbint/stbgho.src
source/fcm/stbgho.fcm
Files Modified:
source/sccdftbint/sccdftbini.src
source/sccdftbint/sccdftbsrc/eglcao.f
source/sccdftbint/sccdftbsrc/gradient.f
source/sccdftbint/sccdftbsrc/mulliken.f
source/sccdftbint/sccdftbsrc/repulsive.f
source/gener/update.src
..............................................................................
1.11.2 Recentering Bug fix
A bug has been fixed for the reCENTering utility that allows to
recenter the system at the geometric center of the first NCRES residues
in the psf file. A redundant section of the code has been commented out.
File Modified:
source/dynamc/dcntr1.src
..............................................................................
1.11.3 MO Transformation Bug fixed
In the GHO implementation for the semiempirical QM module, a bug
has been fixed for the transformation of the molecular orbitals (MOs)
from the hybrid orbital (HO) basis to the atomic orbital (AO) basis
when more than one GHO boundary atoms are involved. Although this bug
did not affect results of energies, gradients, and atomic Mulliken
charges, it may potentially cause problems if the MOs (obtained from a
multi-boundary GHO calculation) are further used by other routines
for other purposes.
File Modified:
source/quantum/qmset.src
------------------------------------------------------------------------------
1.12 SASA Changes and Enhancements
Developers : Urs Haberthuer and Amedeo Caflisch
Email Address : atlantis@bioc.unizh.ch, caflisch@bioc.unizh.ch
Institution : University of Zurich, Switzerland
Date : July 3, 2004
The keywords to modify the SASA parameters from within the CHARMM input
file were changed for clearer usability. This concerns the keywords to
modify the radii, probabilistic parameters, and connectivity parameters
for the surface calculations. The keywords to modify the surface-tension
like solvation parameters were also changed. See the SASA documentation
for the new syntax.
Two keywords, INFX and SURF, were added. INFX causes the fixed exclusion
atoms to be considered for the surface calculations. (By default, they
are neglected for historical reasons. See the SASA documentation for
more detailed explanations.) SURF causes the approximated atomic solvent
accessible surface areas to be stored in WMAIN.
Lazaridis and coworkers introduced the CHARMM atom type CR in
param19_eef1.inp and toph19_eef1.inp. This atom type is now considered
explicitly in the SASA code although all the SASA parameters for CR are
identical to those for the CHARMM atom type C.
Some code cleanup and adjustments of the documentation within the SASA
code were performed.
Files Modified:
doc/sasa.doc
source/fcm/sasa.fcm
source/misc/sasini.src
source/misc/sasene.src
2.1.1 Rotational, Translational and Vibrational Entropy
Calculation of rotational, translational and vibrational entropy is added.
The rotational and translational components are calculated in manip/rgyr.src
and vibrational component of entropy is calculated in vibran/vibsub.src.
Entropy keywords are read in manip/corman.src (as an extention to the COOR
command) and in vibran/vibran.src (as an extension to VIBRan DIAG command).
The VIBRan command is invoked to calculate all three entropy components
(rotational, translational, and vibrational). VIBRAN will perform vibrational
entropy calculation and will call CORINER subroutine to perform calculation of
rotational and translational components. When invoked from the COOR command
only rotational and translational entropy components will be calculated.
Files Added:
source/fcm/entropy.fcm
Files Modified:
source/manip/corman.src
source/manip/rgyr.src
source/vibran/vibran.src
source/vibran/vibsub.src
doc/corman.doc
doc/vibran.doc
doc/subst.doc
New Testcase:
test/c32test/entropy.inp
..............................................................................
2.1.2 ESP Charge Fitting and Drude Polarizability Determination
Charge fitting capability is introduced into the misc module
(with Guillaume Lamoureux).
Files Added:
source/misc/fitcharge.src
Files Modified:
source/charmm/charmm_main.src
New Documentation:
doc/fitcharge.doc
New Testcase:
test/c32test/cyt_chgfit.inp !CHARMM input file
test/data/cyt_chgfit.pot !input data
test/data/cyt_chgfit.pot0 !input data
test/data/cyt_chgfit.qpos !input data
..............................................................................
2.1.3 Flexible Format for Printing Vibrational Frequencies
Printing vibrational frequencies for a very large molecule causes
format overflow in the field of "mode number" for systems larger
than 3333 atoms. This is because the i4 format allows printing of 9999
modes only. To fix this problem a flexible format was implemented,
which changes the format specification depending on the number of modes
to print. The i4 format is kept for systems up to 3333 atoms. The
extended format is aplied to larger systems changing the format
specification based on number of modes to print. The printing
function (subroutine) FREQPR is added to vibran/vibutil.src
Files Modified:
source/vibran/quasi.src
source/vibran/rbquas.src
source/vibran/redbas.src
source/vibran/vibsub.src
source/vibran/vibutil.src
..............................................................................
2.1.4 Numerical Vibrational Analysis with SCF Drudes
Regular vibrational analysis treats Drude particles as real atoms and
thus shows extra peaks on the IR-spectrum due to the Drude particles. This
complicates CHARMM IR-spectrum comparison with QM or experimental data.
The purpose of this addition is to allow vibrational spectrum analysis
for molecules in the presence of Drude particles to be conducted in such
a way that Drude particles will not be present in the IR-spectrum. This
regimen is called SCF Drudes where the position of Drude particles is
instantenously adjusted to any rearrangement in ithe position of real atoms.
Second derivatives are calculated by using finite differences applied to
real atoms and followed by Drude coordinate relaxation after every change in
coordinates of real atoms. This way Drude degrees of freedom are projected
onto the second derivatives of the real atoms.
New logical variable LDSCF was introduced to VIBRAN subroutine.
This keyword is set .TRUE. by presense of newly introduced DSCF keyword
to VIBRAN as an extention to the DIAG subcommand. Since Drude particles
are treated in the SCF regimen the mass assigned to Drude particles is
moved back to the corresponding real atom. The initial masses of real
atoms and Drude particles are backed up in the temporary array BAM
having size BSPACE:
Files Modified:
source/vibran/vibran.src
source/vibran/vibsub.src
source/vibran/raise.src
source/vibran/vibcom.src
doc/vibran.doc
New Testcase:
test/c32test/dscfvib.inp
..............................................................................
2.1.5 MOLVIB Analysis with Drudes
Regular MOLVIB analysis does not support the classical Drude oscillator
polarizable model. The support was added by calculating numerical second
derivatives under the condition of SCF Drudes and passing the resized
second derivative matrix and coordinates and masses of real atoms to the
MOLVIB subroutine. This approach is invoked automatically in the presence of
Drude particles.
Files Modified:
source/molvib/molvco.src
source/molvib/molvsb.src
doc/molvib.doc
New Testcase:
test/c32test/dmolvib.inp
..............................................................................
2.1.6 COOR MAXDIST
The command computes the MAXIMUM distance between two selected sets
of atoms. Similar to the COOR MINDIST command. Calls to SUBROUTINE DISTAN
have been modified to include an additional logical variable MAXD
Files Modified:
manip/corman.src
manip/corman3.src
doc/corman.doc
------------------------------------------------------------------------------
2.2 TSRI Developments
Developers : Mike Crowley and Charles L. Brooks, III
Email Address : crowley@sripps.edu, brooks@scripps.edu
Institution : The Scripps Research Institute
Date : December 30, 2004
2.2.1 AFM Reset
The reset command is added to afm. This permits the afm commend to
be run in a loop with all data structures cleared in between.
Files modified:
doc/afm.doc
source/energy/afm.src
source/fcm/afm.fcm
..............................................................................
2.2.2 Clean-Up
Some code cleanup and prefx labeling to make debugging easier.
Files modified:
source/energy/energy.src
source/energy/eutil.src
source/nbonds/enbfast.src
source/util/prpref.src
..............................................................................
2.2.3 GBMV Bugfix
We fixed a number of issues related to the performance and correctness of
the GBMV code on serial and parallel machines.
Files modified:
source/energy/gbmv.src
source/fcm/gbmv.fcm
..............................................................................
2.2.4 Huge Version
HUGE keysord added to code and install.com for million atom systems.
Files modified:
install.com
source/fcm/dimens.fcm
source/fcm/heap.fcm
source/fcm/stack.fcm
..............................................................................
2.2.5 Makefile Update
Updated osx and gnu Makefiles
Files modified:
build/UNX/Makefile_osx
build/UNX/Makefile_gnu
..............................................................................
2.2.6 Testcase Fixes
Small fixes to test cases to correct poor design of some test cases and
to add some functionality to others.
Files modified:
test/c31test/nebdiala.inp
test/c31test/afm.inp
test/c31test/nebdialapmf.inp
test/c31test/off_path_simulation.inp
..............................................................................
2.2.7 Timing Fixes
Timer debugging added to prevent double timing and other timing errors.
Files modified:
source/fcm/new_time.fcm
source/util/new_timer.src
------------------------------------------------------------------------------
2.3 Developments at the National Institute of Health
Developers : H. Lee Woodcock, Xiongwu Wu and Bernard R. Brooks
Email Address : hlwood@nih.gov, wuxw@nhlbi.nih.gov, brb@nih.gov
Institution : Laboratory of Biophysical Chemistry, NHLBI, NIH
Date : December 20, 2004
2.3.1 Molecular Modeling with Map Objects
The EMAP module is expanded to energy-based map object modeling.
The concept of field maps is introduced to describe electrostatic field of
a molecular system. The field map and density map, as well as the core map
provide a way to evaluate energies between map objects. Based on energies,
map objects can be used to search low energy conformations of macromolecular
assemblies.
Files Added:
source/emap/emapfield.src
Files Modified:
source/fcm/emap.fcm
source/emap/emapsubs.src
source/emap/emapop.src
source/emap/emapdock.src
source/emap/emapio.c
doc/emap.doc
doc/io.doc
New Testcase:
test/c32test/dock_with_maps.inp
test/data/tcr.pdb
..............................................................................
2.3.2 IPS Enhancement for 2D Homogenous Systems
IPS pressure tensions are calculated based on homogenous directions for
surface tension calculation. 2D IPS routines are added for faster calculation.
Files Modified:
source/fcm/nbips.fcm
source/energy/energy.src
source/nbonds/enbond.src
source/nbonds/enbips.src
source/nbonds/nbutil.src
source/nbonds/pmeutil.src
doc/nbonds.doc
test/c32test/ips_tip216.inp
..............................................................................
2.3.3 SGLD Improvements
The guiding force calculation in routine SGLDW is improved. An input
parameter, TEMPSG, is added SGLD algorithm for MD simulation is added as SGMD
Files Modified:
source/fcm/sgld.fcm
source/dynamc/sglds.src
source/dynamc/dcntrl.src
source/dynamc/dynamc.src
doc/sgld.doc
test/c31test/sgld.inp
..............................................................................
2.3.4 Replica Path and Off-Path Simulation Enhancements
(Lee Woodcock and Milan Hodoscek)
Defined maximum number of replicas allowed (1000). Added the ability to
restart off-path simulations from previous run. Must use restart file for
this. Once off-path simulations is done potential of mean force is written
out to a file (pmf.dat).
Files Modified:
source/energy/epath.src
source/fcm/path.fcm
source/dynamc/dynio.src
..............................................................................
2.3.5 QM/MM Improvements
1. Added noguess option to running parallel replica path with Q-Chem
2. Removed obsolete variables and comments
3. Fixed QM force manipulation
4. Fixed SCF convergence error printing
5. Fixed Sodium definition in Findel (Lee and Milan)
Files Modified:
source/gukint/gukini.src
source/quantum/addlnat.src
source/fcm/gamess.fcm
..............................................................................
2.3.6 Free Energy Perturbation Bug Fixes
1. Fixed data structure problem: SPPSFT was not being set properly
2. Added memory allocation and correct filling for things defined in the
data structures
Files Modified:
source/pert/pert.src
source/fcm/pert.fcm
..............................................................................
2.3.7 Added QM/MM Free Energy Pertubation (with Q-Chem)
1. Added Mass to PERT data structure
2. Modified GUKENE and QCHEM subroutines and calls
3. Added QM/MM energy calls to epert routines
4. Fixed QCHEM subroutine to use both lambda 0 and lambda 1 PSF
5. Added XX as an atom type to Findel: this represents a quantum dummy atom
6. Added test case for QM/MM free energy perturbation
Files Modified:
source/gukint/gukini.src
source/nbonds/nbonds.src
source/quantum/addlnat.src
source/energy/energy.src
source/pert/epert.src
source/pert/pert.src
source/fcm/pert.fcm
Files Added:
test/cquantumtest/qmmm_pert.inp
test/data/qmmm_pert.inp
test/data/s0.inp
test/data/s1.inp
------------------------------------------------------------------------------
2.4 Developments at NIC-Slovenia
Names : Milan Hodoscek
Email Address : milan@cmm.ki.si
Institution : National Institutes of Chemistry, Ljubljana, Slovenia
Date : December 30, 2004
2.4.1 New Reaction Coordinate added to Biased MD
The helix expansion reaction coordinate was added to the HQBM
module.
Files modified:
source/energy/hqbm.src
source/fcm/hqbm.fcm
2.4.2 Replica Path fixes.
The problem with parallel and scalar QM/MM replica path method is
fixed
Files modified:
source/energy/ecnstr.src
source/energy/epath.src
source/fcm/parallel.fcm
source/machdep/paral1.src
2.4.3 GAMESS QM/MM DFT speedup
The new GAMESS DFT SCF convergency enhancement is switched off
when using NOGUess keyword, which significantly speeds up the
calculations.
Files modified:
source/fcm/gamess.fcm
source/gukint/gukini.src
2.4.4 New version of GAMESS is supported in CHARMM
Version of GAMESS 22 November 2004 R1 is now supported with
CHARMM. New in this version are faster two electron integral code, and
QFMM derivatives.
Files modified:
source/gamint/ddi.src
source/gamint/gamess/gamess.src
source/gamint/gamess/grd1.src
source/gamint/gamess/grd2a.src
source/gamint/gamess/guess.src
source/gamint/gamess/inputa.src
source/gamint/gamess/inputb.src
source/gamint/gamess/inputc.src
source/gamint/gamess/int1.src
source/gamint/gamess/iolib.src
source/gamint/gamess/mccas.src
source/gamint/gamess/prpel.src
source/gamint/gamess/prplib.src
source/gamint/gamess/prppop.src
source/gamint/gamess/rhfuhf.src
source/gamint/gamess/scflib.src
source/gamint/gamess/unport.src
2.4.5 LONEPAIR in PSF fix
If LONEPAIR is not specified in pref.dat psfres.src doesn't
compile. Also reading PSF files in this case was not correct. Fixed
now.
Files modified:
source/io/psfres.src
2.4.6 Parallel fixes
Debug output removed in paral2.src. Some machines can't compile
TCP/IP socket code, so it is removed unless specified in pref.dat
Some parallel libraries don't remove the command line
parameters. There can be more than 30 so maximum is increased to 300
Files modified:
source/machdep/paral2.src
source/machdep/socket.c
source/machdep/startup.src
install.com
2.4.7 Writing of the trajectories from MINI CONJ
Support to write trajectory files from MINI CONJ
calculations. Mainly used for QM/MM.
Files modified:
source/minmiz/conjug.src
------------------------------------------------------------------------------
2.5 Developments at Cornell University
Developers : Yuqing Deng, Guillaume Lamoureux, Igor V. Vorobyov and
Benoit Roux
Email Address : yud2001@med.cornell.edu, Guillaume.Lamoureux@cornell.edu
benoit.roux@med.cornell.edu
Institution : Weill Medical College of Cornell Univeristy
Date : December 21, 2004
2.5.1 WCA Separation of LJ potential
The LJ potential is spit into repulsive and attractive parts in EGROUP.
Three addition arguments are added to EGROUP. A new scalar WCAD is introduced
in the PSF, which is used to scale the WCA-attractive potential.
The manipulation of WCAD is implemented analogous to RSCALF. Two logicals
(scl0, scl1) and floating point arguments (scr0, scr1) are introduced in
the PERT command line for progressively turning on WCA-repulsion in
free energy calcualtion.
Two arguments (EMP1, EMP2) are introduced in the SSBP MMFP command line
for empirical correction of SSBP. The empirical correction can be turned on
and off with EMPI and NEMP, respectively. PERT command stores the selected
atoms (in PERT command line) in an array and these are used in EPERT to
calculate long-range correction for SSBP free energy.
Three miscellaneous energy variables are added:
WHAMFE, total free energy of WHAM
SSBPLRC, long-range free energy correction for SSBP
SSBPLRCS, standard deviation of SSBP long-range correction
Files Modified:
source/charmm/charmm_main.src
source/charmm/iniall.src
source/emap/emapsubs.src
source/energy/energy.src
source/energy/intere.src
source/fcm/dimens.fcm
source/fcm/pert.fcm
source/fcm/psf.fcm
source/fcm/ssbp.fcm
source/gener/drude.src
source/gener/genpsf.src
source/gener/modpsf.src
source/gener/replica.src
source/image/eimage.src
source/image/upimag.src
source/io/psfres.src
source/manip/scalar.src
source/mbond/mbdiag.src
source/mc/mcener.src
source/mc/mcimge.src
source/misc/ssbp.src
source/misc/xray.src
source/nbonds/enbond.src
source/nbonds/enbondg.src
source/pert/epert.src
source/pert/icfcnf.src
source/pert/icpert.src
source/pert/pert.src
source/pert/tsme.src
source/pert/wham.src
source/quantum/addlnat.src
source/quantum/qmene.src
source/shapes/mdlio.src
source/util/selcta.src
source/vibran/vibblock.src
doc/mmfp.doc
doc/pert.doc
doc/scalar.doc
doc/subst.doc
New Testcase:
test/c32test/attr.inp
test/c32test/repul.inp
test/data/pert.prt
..............................................................................
2.5.2 Code Cleanup and Bug Fixes in TPCONTROL and DYNA VV2
For constant-pressure simulations containing Drude oscillators,
the TPCONTROL command is now scaling the Drude--atom distances
(i.e., the dipoles) along with all other bonds. This behavior could be
obtained in the previous version of the code by using the non-documented
"DSCY" flag, but it was not the default. (BUGFIX, tpcontrol.src)
The dimensions of the crystal cell (?XTLA, ?XTLB, ?XTLC) were not
updated after a call to DYNA VV2. (BUGFIX, dcntrl.src)
are.
Some inessential parts of the VV2 subroutine were never fully functional.
They have been removed. (CODE CLEANUP, dynamvv2.src)
The SCF treatment of Drude oscillators implemented for DYNA LANG was
"forgetting" the special nature of Drude particles after exiting the DYNAMC
subroutine, resulting in a crash at restart. (BUGFIX, dynamc.src)
Files Modified:
source/dynamc/dcntrl.src
source/dynamc/dynamc.src
source/dynamc/dynamvv2.src
source/dynamc/tpcontrol.src
------------------------------------------------------------------------------
2.6 Karolinska Institute Fixes and Enhancements
Developer : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska Institute
Date : December 30, 2004
2.6.1 Minor modifications/fixes
(1) SINGLE precision version cannot be created due to use of non-generic
forms of intrinsic functions in several routines. I updated prefx.src with
these, and also had to make some changes to source files.
CHARMM created with SINGLE in pref.dat is however NOT fully functional.
Timing routines (elapsed time) do not work, parallel jobs hang (I only tried
socket communication), charges do not sum up correctly at psf generation;
there may be other problems as well. It would be useful to have this
working correctly again.
Files modified:
tool/prefx.src
source/adumb/eadumb.src
source/emap/emapdock.src
source/util/selcta.src
(2) Set values of BOMLEV, IOLEV, PRNLEV variables at startup, corrected
a typo in FTCPWRT call
Files modified:
source/charmm/charmm_main.src
(3) Added SURFace-area timeseries to correl.src and allow output of long
lines to data files if LONG command is in effect.
Files modified:
source/correl/correl.src
source/correl/anacor.src
source/correl/corrio.src
source/manip/corman.src
source/misc/surfac.src
doc/correl.doc
(4) Allow echeck to be turned off by specifying a negative value; not
documented.
Files modified:
source/dynamc/dynamc.src
(5) Some format changes to allow for large step numbers to print correctly.
Files modified:
source/dynamc/dynsub.src
(6) Format change to allow larger heap allocations to be correctly reported.
Files modified:
source/machdep/space.src
(7) Collect histograms of hydrogen-bond length and lifetime distributions in
COOR HBOND.
Files modified:
source/manip/hbanal.src
doc/corman.doc
Files added:
source/fcm/hbanal.fcm
(8) Modification of log-file handling in install.com to log the output from
the current compile/link to build//new.log, which is appended to
build//.log.
Files modified:
install.com
(9) Added keyword DEBUG to install.com - this sets enviroment variable DEBUG,
which is parsed by Makefile_gnu to use the debugging definition of the
compile command FCD.
Files modified:
install.com
build/UNX/Makefile_gnu (also contains some intel fortran flag changes)
..............................................................................
2.6.2 SOLVENT-SOLVENT interaction routine
Experimental water-water interaction routine for CHARMM c32a1.
Depending on the size of the system and the number of water molecules,
speedups in the range of 2-5 fold may be obtained. Non-bonded interactions
within a user specifed selection of water molecules (any three site water
model with the oxygen first in the PSF should work) are removed from the
regular non-bonded lists and are instead handled by a dedicated routine.
Pref.dat The code is protected by keyword SLVSLV
Modified files:
source/energy/energy.src
source/image/upimag.src
source/image/eimage.src
source/charmm/miscom.src
source/charmm/iniall.src
source/nbonds/nbonds.src
build/gnu/nbonds.mk incomplete, just compiles ewwnb.src,
but there are no checks on wwnb.fcm
doc/nbonds.doc
New files:
source/nbonds/ewwnb.src routines for setup, space allocation,
and the energy calculation
source/fcm/wwnb.fcm
test/c32test/nbsolv.inp
test/output/nbsolv.out output from nbsolv.inp using c32a1
ifort v8 on RH9 GNU/Linux
..............................................................................
2.6.3 Partial Table Lookup
For the distance dependent parts of the Coulomb and van der Waals forces,
for all interactions. Moderate speedup (10-20%).
Protected by LNTAB1 in pref.dat.
Files modified:
source/charmm/iniall.src
source/energy/energy.src
source/nbonds/enbaexp.src
source/nbonds/nbutil.src
source/nbonds/nbonds.src
doc/nbonds.doc
New files:
source/nbonds/ewwnb.src
sourc/fcm/wwnb1.fcm
------------------------------------------------------------------------------
2.7 Multiple and Moving Point NOEs
Name : Michael Schaefer
Email Address : michael.schaefer@syngenta.com
Institution : Syngenta Crop Protection AG, Basel
Date : 27.12.2004
The previous PNOE implementation would allow for a single point-NOE
only (an NOE between an atom or group of atoms, and a single point
in space). This has been generalized to allow for multiple point-NOE's,
just like normal atom(group) -- atom(group) NOE's. The documentation
does not require change in this respect, as it appeared to suggest
that multiple PNOE's are possible.
To further enhance the capabilities offered by the PNOE scheme,
the NOE facility now offers the option of moving point-NOE's,
with a predefined set of of starting points, target points, and
a number of dynamics or minimization steps over which the PNOE's
are to move.
Minor bugs related to PNOE's have been fixed, e.g., the distribution
of data to all nodes in parallel mode, or the read/write of NOE
data concernign PNOE's where the J-atom list is irrelevant (it
is a point).
Files Modified:
source/adumb/eadumb.src
source/charmm/iniall.src
source/energy/energy.src
source/fcm/noe.fcm
source/mc/mc.src
source/mc/mcener.src
source/misc/genetic.src
source/misc/noe.src
source/pert/epert.src
doc/cons.doc
New Testcase:
test/c32test/pnoe.inp
------------------------------------------------------------------------------
2.8 SASA Enhancements and Bugfixes
Developers : Urs Haberthuer, Riccardo Pellarin, and Amedeo Caflisch
Email Address : atlantis@bioc.unizh.ch, pellarin@bioc.unizh.ch,
caflisch@bioc.unizh.ch
Institution : University of Zurich, Switzerland
Date : December 30, 2004
(1) New Surface Parameters
A new keyword, NEWP, is added. It triggers the use of a new set of
values for the radii, probabilistic parameters, and connectivity
parameters. (These parameters are used to calculate atomic solvent
accessible surface areas within the SASA module.) The new set was
derived in 2002 by Haberthuer and it gives a better correlation with
exact analytical surfaces than the original Hasel and Still surface
parameters.
(2) Images
Image lists are now supported in SASA. This allows to use SASA for
simulations with periodic boundary conditions.
(3) Documentation
The SASA documentation itself and also the documentation within the
SASA code is updated.
(4) Miscellaneous
The atom type C1ES is now supported by SASA and the format of the output
of the SASA module slightly changed.
(5) Bugfixes
The SASA module did not work correctly for simulations with constant
pressure since the call to the subroutine SASENE in the subroutine
ENERGY was at the wrong place. This has been corrected.
An empty nonbond exclusion pair list could crash the SASA module. This
bug is now fixed.
Files Modified:
doc/sasa.doc
source/energy/energy.src
source/fcm/sasa.fcm
source/misc/sasini.src
source/misc/sasene.src
The following are enhancements and bugfixes of the development period
from February 15, 2005 through August 15, 2005. The developments are
based on CHARMM version c32a2.
3.1 General compilation of SCC-DFTB in CHARMM
Developers : Qiang Cui
Email Address : cui@chem.wisc.edu
Institution : University of Wisconsin, Madison
Date : July 1, 2005
"$(LIB)/sccdftbint.a" is added to all platform Makefiles of
build/UNX. Otherwise, SCC-DFTB will NOT be compiled even with the T keyword.
Files Modified:
install.com
------------------------------------------------------------------------------
3.2 TSRI Cleanup and Bugfixes
Developers : Mike Crowley, Charles L. Brooks, III
Email Address : crowley@sripps.edu, brooks@scripps.edu
Institution : The Scripps Research Institute
Date : June 30, 2005
Files Modified:
source/dynamc/dynamc.src some pref labels added
source/emap/emapfield.src removed extraneous "+" characters and fixed heap call
source/energy/gbmv.src bugfixes
source/fcm/gbmv.fcm bugfixes
source/gener/mkpres.src bugfix format statement
source/io/rtfio.src very minor cleanup
source/manip/shake.src cleanup and remove PARASCAL code for fast shake
source/manipfsshake.src
source/misc/mmfp.src bugfix format statement
source/misc/pbeq.src bugfix format statements
------------------------------------------------------------------------------
3.3 Developments at the National Institute of Health
Developers : Jhih-Wei Chu, H. Lee Woodcock, Xiongwu Wu and
Bernard R. Brooks
Email Address : chu@hec.utah.edu, hlwood@nih.gov, wuxw@nhlbi.nih.gov,
brb@nih.gov
Institution : Laboratory of Biophysical Chemistry, NHLBI, NIH
Date : July 1, 2005
3.3.1 NEB minimization problem fix
The SD code is modified so that it can be used with NEB. "If(QPNEB)" is
used to separate the NEB related code and the original part. NEB related parts
in epath.src and energy.src are modified to make sure the NEB method works
(the NEBF command).
Warning added when NEB+climbing image is used together in ABNR.
Files Modified:
source/energy/energy.src
source/energy/epath.src
source/minmiz/steepd.src
source/minmiz/abnr.src
Modified Documentation:
doc/minmiz.doc
doc/replica.doc
..............................................................................
3.3.2 IPS Bugfix
For partial homogenous systems (2D as PXY or 1D as PZ), the boundary
energies and forces need to be calculated, which was done by looping over
all atom pairs and is slow. A speed up was done by calculating boundary
forces every NIPSFRQ steps. However, a large NIPSFRQ introduces large errors
in the calculation results.
This fix changes the way in which boundary energies and forces are
calculated so that the calculation is very efficient and can be done every
dynamcs step without significantly slowing down a simulation. NIPSFRQ is set
to 1 by default and can be set to large values for simulations where
conformational change is slow.
Files involved:
source/fcm/nbips.fcm Updated common variables
source/energy/energy.src Modified parallelization for EXIPS, EXIPS2D,
and EXIPS3D calculation.
source/nbonds/enbond.src Changes in ENBIPS2D arguments.
source/nbonds/enbonda.src Common variable updates.
source/nbonds/enbondg.src Common variable updates.
source/nbonds/enbfast.src Common variable updates.
source/nbonds/enbips.src Change the way in which IPSSYS and IPSSYS2D
is calculated.
source/quantum/qmene.src Change to make consistant in ENBOND arguments.
------------------------------------------------------------------------------
3.4 IBM Pwr4 Port
Names : Milan Hodoscek
Email Address : milan@cmm.ki.si
Institution : National Institutes of Chemistry, Ljubljana, Slovenia
Date : June 30, 2004
Support for parallel CHARMM on IBM power4 CPU architecture using
GNU/Linux as an operating system.
Files Added:
build/UNX/Makefile_ibmlnxmp
tool/ibmlnxmp_fixlibs
Files Modified:
source/energy/rmsd.src
source/machdep/cstuff.c - one #if
source/machdep/machio.src - order changed for ##IF
doc/parallel.doc
install.com
------------------------------------------------------------------------------
3.5 Developments at Cornell University
Developers : Edward Harder, Hyung-June Woo, Jose D. Faraldo-Gomez,
Yuqing Deng, Benoit Roux
Email Address : edh2004@med.cornell.edu, woo@chem.unr.edu,
jdf2002@med.cornell.edu, yud2001@med.cornell.edu,
benoit.roux@med.cornell.edu
Institution : Weill Cornell Medical College
Date : June 25, 2005
3.5.1 The Drude mass dependence bugfix
This fixes bugs for the Drude mass dependance when using SCF dynamics
and another bug for restarting of VV2 dynamics in the NVE ensemble.
When simulating drude models using the SCF evaluation of the drude particle
positions (drude mass independant) the trajectories were dependent on the
drude mass. Also, VV2 dynamics using no thermostat and no barostat couldn't
be restarted. Subroutine READYN would complain about an "EOF during read".
Files involved:
source/dynamc/dcntrl.src
source/dynamc/dynamc.src
..............................................................................
3.5.2 Dipole time series bugfix
Dipole time series produced is incorrect for use in the calculation
of the dielectric constant. If MAXA is not set in the input file the default
maximum atom selection is arbitrarily set to 100 which is often insufficient
for calculating bulk dipole moment time series. To fix this the default value
has been set to the number of atoms in the system "NATOM".
Files involved:
source/correl/correl.src
------------------------------------------------------------------------------
3.6 Karolinska Institute Fixes and Enhancements
Developer : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska Institute
Date : June 30, 2005
1) Modification. Allow a subset of a timeseries to be copied in CORREL
MANTIM COPY.
Files Modified:
source/correl/mantim.src
doc/correl.doc
2) Bugfix: Calling sequence to ALLHP wrong in emapfield.src
File modified:
source/emap/emapfield.src
3) Bugifx: Protect parllel comm call from being executed when not needed.
ECONT array only needs to be distributed when QECONT is true.
Files Modified:
source/energy/energy.src
4) Bugfix: Coding error for the new RECT crystal type.
Files Modified:
source/image/crystal.src)
5) Bugfix. Array dimensions were wrong, and part of the logic flawed for the
check that the main axis did not swap direction 180 degrees, in the code to
return all three axes for the inertial moment timeseries
(ENTER ... INER ALL). Some new code added to check for axis swap for the
other two axes as well.
Files Modified:
source/correl/anacor.src
doc/correl.doc
6) Minor modifications.
Files Modified:
install.com Updated options for SCALI; set chmsocket for cc
as well as gcc when needed
source/nbonds/ewwnb.src Output format change in informational message
doc/io.doc Clarification of WRITE/PRINT NBOND and
keyword FIRST for WRITE COOR PDB FIRST
test/c32test/dscfvib.inp Corrected erroneous use of ?vibran .ne. 1
test/c32test/entropy.inp (should be ?novibran .eq. 1)
------------------------------------------------------------------------------
3.7 University of Chicago Bugfixes
Developers : Aaron R. Dinner
Email Address : dinner@uchicago.edu
Institution : The University of Chicago
Date : June 30, 2004
(1) Memory allocation error fix
Scratch arrays are allocated for charge equilbration during the
DYNAMC call but not freed. In addition to memory leak, arrays are allocated
as HEAP then used as STACK.
Files involved:
source/mc/mvhmc.src
(2) RXNCOR fix
Forces but not energies from umbrella potential term are added to totals.
Umbrella potential term is not added to total energy or printed.
Added UMBR to ETERM array and made corresponding changes in energy utilities.
Files involved:
source/energy/energy.src
source/energy/eutil.src
source/energy/printe.src
source/fcm/energy.fcm
source/fcm/rxncom.fcm
source/rxncor/rxnene.src
(3) MC fix for MVTYP GCMC and GRID/CBIAS
Error-check for no blockers is done before counting them.
Files involved:
source/mc/mvgcmc.src
(4) GCMC counter fix
GCMC counters not updated when runnning with finite rather than
periodic boundary.
Files involved:
source/mc/mcener.src
------------------------------------------------------------------------------
3.8 University of Maryland, School of Pharmacy Developments
Developers : Alex MacKerell, Igor Vorobyov, Victor Anisimov
Pedro Lopes
Email Address : alex@outerbanks.umaryland.edu
Institution : University of Maryland, School of Pharmacy
Date : July 14, 2005
3.8.1 Parameters for classical Drude oscillator model.
Force field parameters for the developmental polarizable model
based on a classical Drude oscillator have been added. Currently,
only parameters for the SWM4-DP water models, alkanes and ions are
available. Toppar files along with example inputs are in the
toppar/drude directory.
3.8.2 Parameters for silicate surfaces.
Force field parameters for silicate and aluminosilicate surfaces
are now availble in the toppar/silicate directory. Included are code
and example inputs to create and generate a quartz 001 surface. Note
that these parameters have been designed to be compatible with the
CHARMM22 and 27 all-atom force fields.
Documentation available in parmfile.doc
------------------------------------------------------------------------------
3.9 Minor Enhancements and Fixes
3.9.1 SPCISM update
Developer : Sergio A. Hassan
Email Address : mago@helix.nih.gov
Institution : CMM/DCB/CIT, National Institutes of Health (NIH)
Date : June 16, 2005
SCPISM doc is updated
File Involved:
doc/scpism.doc
..............................................................................
3.9.2 IMM1 Testcase Updated
Developer : Themis Lazaridis
Email Address : tlazaridis@ccny.cuny.edu
Institution : City College of New York/CUNY
Date : July 12, 2005
The testcase include checking the energy against the expected value.
File Involved:
test/c31test/testimm1.inp
..............................................................................
3.9.3 SHELL Bugfix
Developers : Tibor Rudas, Stefan Boresch
Email Address : tibi@mdy.univie.ac.at, stefan@mdy.univie.ac.at
Institution : Molecular Dynamics and Biomolecular Simulation group
at the Department of Biomolecular Structural Chemistry,
University of Vienna
Date : June 28, 2005
If solvent is decomposed into shells around a solute with shells
extending to less than 8A or to more than 20A the cube size for
the cubing based algorithm is reset. In the former case this leads
(only) to a less efficient - but correct - decomposition while the
generated shells can be incomplete in the latter case.
Files involved:
source/correl/shell.src
..............................................................................
3.9.4 SASA Segmentation Fault Error Fixed
Developers : Riccardo Pellarin and Amedeo Caflisch
Email Address : pellarin@bioc.unizh.ch, caflisch@bioc.unizh.ch
Institution : University of Zuerich, Switzerland
Date : June 21, 2005
When one tries to simulate a sequence that does not contain any TRP or
PHE or TYR, (or in any case where the nonbond explicit exclusion list is empty)
one would get a segmentation fault immediately after the command call.
As an output the following instance error message is normally obtained:
FREHP> sasini.src/SASINI releases 66 words of PXBL at **********
BAD BASE, ********* OR LEN2, 66 PASSED TO FREEHP
However we experienced, in some machines and in some particular compilations,
that program prints only "segmentation fault" or even stops without any alert.
Files involved:
source/misc/sasini.src
..............................................................................
3.9.5 PERT MD Simulation Fix
Developer : Stefan Boresch
Email Address : stefan@mdy.univie.ac.at
Institution : University of Vienna
Date : July 18, 2005
PERT MD runs die with error "GENERATING TOO MANY IM CONTACTS".
Use of PERT automatically disables the BYCB method. Thus, no
BYCB only code should be executed. However, the error
message "GENERATING TOO MANY IM CONTACTS" is triggered by
a sanity check of the BYCB method, which shouldn't be active
in PERT. The code in questions is protected by an ##IF IMCUBES
block, but not protected against being executed if BYCB isn't
used (such as is always the case in PERT runs).
Files involved:
source/nbonds/nbonds.src
..............................................................................
3.9.6 CHARMM Manager's Note
1) SPASIBA force filed code removed
This was not released with c31b1 of August 15, 2004. As it has not been
fixed nor verified, it is not included in the c32b release versions.
2) NBIPS is the default feature of c32b.
The following are enhancements and bugfixes of the development period
from August 15, 2005 through February 15, 2006.
4.1 TSRI Cleanup and Bugfixes
Developers : Mike Crowley, Charles L. Brooks, III
Email Address : crowley@sripps.edu, brooks@scripps.edu
Institution : The Scripps Research Institute
Date : December 31, 2005
- Timer fixes to solve the double-counting problem
- Timer debugging code to check if double-counting or incorrect counting
is suspected
- integer*4 binary I/O enforced.
- f90 compile for sgi IRIX fixes (SFIF90)
[Note: This fails to compile on SGI and is removed. - chmgr ]
- attempt to fix some of the memory hog problems using heap
- Esoteric mpi code for supercomputer center installations:
mpif90 support, memory hog bandaids, eliminate COPYR8, MPI INPLACE
- HUGE size adjustments
Files Added:
build/UNX/Makefile_em64t
build/UNX/Makefile_itanium
Files Modified:
build/UNX/Makefile_gnu
build/UNX/Makefile_ibmaix
build/UNX/Makefile_ibmaixmp
build/UNX/Makefile_osx
doc/cheq.doc
source/cff/parrdr_cff.src i4 binary
source/correl/solana.src SGIF90
source/dynamc/cveloci.src memory hog fix use heap
source/dynamc/dynamc.src Timer fixes, mpiall, cheq
source/dynamc/dynio.src i4binary fix
source/dynamc/mts.src memory hog
source/energy/energy.src timer fixes,mpiall
source/energy/epath.src SGIF90
source/energy/eutil.src timer fix
source/energy/gbmv.src SGIF90
source/energy/hqbm.src memory hog
source/fcm/cveloci.fcm memory hog
source/fcm/gbmv.fcm declaration fix
source/fcm/new_time.fcm timer fixes
source/fcm/pme_par.fcm increase node limit to 512 for parallel pme
source/fcm/stack.fcm HUGE size adjustment
source/image/upimag.src extra info for bomb from exceeding limits
source/io/psfres.src CHEQ bug fixes
source/machdep/machutil.src bug fixes, added support for using mpif90 instead
of specific compiler name so it will find mpif.h,
support for ia64 mpi
source/machdep/paral1.src mpif90
source/machdep/paral2.src mpif90
source/machdep/paral3.src mpif90
source/machdep/startup.src change for HUGE and itanium header
source/manip/shake.src size overflow protection and mpif90
source/minmiz/abner.src ##IF fix
source/misc/surfac.src size HUGE added
source/nbonds/enbond.src timer fix
source/nbonds/ewald.src CHEQ fix
source/nbonds/nbutil.src memory hog bandaid
source/nbonds/pmeutil.src node limit increased, mpif90 support
source/util/new_timer.src timer debugging added
source/util/title.src testendian fixes
------------------------------------------------------------------------------
4.2 Developments at the National Institute of Health
Developers : H. Lee Woodcock, Xiongwu Wu and Bernard R. Brooks
Email Address : hlwood@nih.gov, wuxw@nhlbi.nih.gov, brb@nih.gov
Institution : Laboratory of Biophysical Chemistry, NHLBI, NIH
Date : December 31, 2005
4.2.1 EMAP I/O and Command fixes
The CCP4 map head data format is corrected. Map operation bugs are fixed
Files involved:
source/emap/emapio.c
source/emap/emapop.src
source/emap/emapsubs.src
source/emap/emapdock.src
source/fcm/emap.fcm
doc/emap.doc
..............................................................................
4.4.2 Bugfix for guiding temperature calculation
Guiding temperature calcuation is corrected based on friction costant,
local average time, and local average of guiding force products.
Files involved:
source/dynamc/dcntrl.src
source/dynamc/dynamc.src
source/dynamc/sglds.src
source/fcm/sgld.fcm
test/c31test/sgld.inp
doc/sgld.doc
..............................................................................
4.2.3 QM/MM Q-Chem interface
Point charge gradient were being ignored if they occured after the QM
region in the psf. This was fixed. Also, fixed a bug associated with how
Q-Chem/CHARMM handled MP2 and RIMP2 QM calculations.
Files involved:
source/fcm/gamess.fcm Added stuff to handle RIMP2 QM calculations
source/gukint/gukini.src Fixed reading of point charge gradients.
..............................................................................
4.2.4 image and nonbond commands
The problem is that when using 'cons fix' some atoms non-bonded
interactions (with other fixed atoms) are still computed even when they are
fixed. In particular, in the first bug the loop which identifies atoms that are
fixed misses the first fixed atom of each group, in the second bug the 'expand'
option is not correctly conditioned on 'imove'.
Files involved:
source/nbonds/nbonda.src Added imove to the expand keyword test
source/image/nbondm.src Set QMOVE to true
------------------------------------------------------------------------------
4.3 Karolinska Institute Fixes and Enhancements
Developer : Lennart Nilsson
Email Address : Lennart.Nilsson@biosci.ki.se
Institution : Karolinska Institute
Date : December 30, 2005
4.3.1 64-bit space allocation
From Bogdan's report.
Files involved:
source/machdep/space.src
..............................................................................
4.3.2 Bugfixes
1) The DONOr/ACCEptor commands did not work correctly in ADD mode.
Also clarified documentation.
Files involved:
source/gener/hbonds.src
doc/hbonds.doc
2) The code to correct inadvertent reordering of the minor inertial axes in
CORREL timeseries INERtia ALL has been corrected.
Files involved:
source/correl/anacor.src
3) Fix the workings of selections and orientating structures in CORREL
timeserise RMS
Files involved:
doc/correl.doc
4) Fast SHAKE bugfix (charmm.org)
Files involved:
source/manip/fsshake.src
5) PERT SSBP long range correction bugfix (charmm.org)
Files involved:
source/pert/pert.src
