--------------------------------------------------------------------------- CHARMM22.0.b Release April 22, 1991 CHARMM22.0.b1 Release September 30, 1991 CHARMM22 Release January 1, 1992 c22g1 Release February 15, 1992 c22g2 Release July 7, 1992 CHARMM23.0 c23a1 Developmental August 15, 1992 c23a2 Developmental October 25, 1992 c23f Developmental March 1, 1993 c23f1 Developmental March 15, 1993 c23f2 Developmental August 15, 1993 c23f3 Release February 1, 1994 c23f4 Release August 15, 1994 c23f5 Release March 15, 1995 CHARMM 24.0 c24a1 Developmental February 15, 1994 c24x1 Evaluation February 15, 1994 c24a2 Developmental August 15, 1994 c24a3 Developmental March 15, 1995 c24b1 Release August 15, 1995 c24b2 Release February 15, 1996 c24g1 Release August 15, 1996 c24g2 Release February 15, 1997 CHARMM 25.0 c25a0 Developmental August 15, 1995 c25a1 Developmental February 15, 1996 c25a2 Developmental August 15, 1996 c25a3 Developmental February 15, 1997 c25b1 Release August 15, 1997 c25b2 Release February 15, 1998 CHARMM 26.0 c26a1 Developmental August 15, 1997 c26a2 Developmental February 15, 1998 c26b1 Release September 30, 1998 c26b2 Release February 15, 1999 CHARMM 27.0 c27a1 Developmental September 30, 1998 c27a2 Developmental February 15, 1999 c27b1 Release August 15, 1999 c27b2 Release February 15, 2000 c27b3 Release August 15, 2000 c27b4 Release February 15, 2001 CHARMM 28.0 c28a1 Developmental August 15, 1999 c28a2 Developmental February 15, 2000 c28a3 Developmental August 15, 2000 c28a4 Developmental February 15, 2001 c28b1 Release August 15, 2001 c28b2 Release February 15, 2002 --------------------------------------------------------------------------- [0] About CHARMM28 Development As an on-going project, CHARMM development will be carried out with CHARMM version 28 series. The base revision c28a1 is the same as c27b1. The following describes new features and enhancements incorporated in the c28 development period. =========================================================================== [1] c28a2 Change Log The following are introduced and modified during the development period of August 15, 1999 through February 15, 2000. 1. University of Maryland Enhancements Name : I-Jen Chen and Alexander D. MacKerell, Jr. Email Address : ijen@outerbanks.umaryland.edu, alex@outerbanks.umaryland.edu Institution : University of Maryland, Baltimore Date : Dec 31, 1999 1.1.1 MMFF Enhancements MMFF module in CHARMM is enhanced to accept molecules in the SYBYL MOL2 format. Molecules of interest can be read in as an integral part of a CHARMM input file (see test/cmmfftest/mmff_mol2.inp and MMFF.DOC USAGE 3c) or as an external MOL2 database file (see test/cmmfftest/mmff_db_1.inp and MMFF.DOC USAGE 3d). Files Modified: source/fcm/exfunc.fcm /io/mainio.src /mmff/merckio.src /mmff.src /util/string.src New Testcases: test/cmmfftest/mmff_mol2.inp /mmff_db_1.inp /data/mmff_db.mol2 Modified documentation doc/mmff.doc .............................................................................. 1.1.2 SOLANA: Rotational Correlation Time of Water Calculation of rotational correlation times corresponding to the three rotational motions of a water molecule has been added to the solvent analysis code. The three rotational motions refer to motion around the dipole axis (twist), around an axis perpendicular to the molecular plane (rock) and around an axis parallel to the H-H vector (wag) (Ref 1). The correlation time is calculated by fitting the exponentional decay part of the corresponding time correlation function C(t) to an exponentional function of the form C(t) = A exp(-t/tau) where tau is the correlation time. The direct correlation functions were calculated via direct method using the CORFUNC subroutine in the CORREL.SRC. The calculation can be invoked by assigning a non-zero integeer value to the keyword RCOR. For the details of input data please see CORMAN.DOC. REFERENCES: 1. Johannesson, H. and Halle, B. J. Am. Chem. Soc. 1998, 120, 6859-6870 2. Wallqvist, A. and Berne, B. J. J. Phys. Chem. 1993, 97, 13841-13851 Files Modified: source/correl/solana.src Testcase Modified: test/c27test/solanal2.inp .............................................................................. 1.1.3 SOLANA: Hydration Number Calculation Calculation of hydration number or, in general, the number of solvent molecules within a specified distance of a multi atom or single atom site has been added to the solvent analysis code. This method counts the number of solvent molecules within RHYD and included normalization for the number of site atoms and time frames. Since this is done within the solvent-site g(r) analysis routine keywords such as ISDIST, MGN, DR and RSPH should be specified. Hydration number calculation can be invoked by specifying a non-zero integer value to the keyword IHYDN. Files Modified: source/correl/solana.src Testcase Modified: test/c27test/solanal2.inp ------------------------------------------------------------------------------ 1.2 Further Enhancements to the Monte Carlo Module Name : Aaron R. Dinner Email Address : aaron@bellatrix.pcl.ox.ac.uk Institution : University of Oxford Date : December 9, 1999 1) Steepest descents minimization prior to application of the acceptance criterion is now allowed. 2) Separate temperatures for each move group are now allowed. 3) NOE constraint terms are now supported. 4) The Tsallis (generalized) acceptance criterion is now allowed. 5) A minor "bugfix" regarding the Delta-E column in the energy table printed during MC: previously, when the running total of the energy and the value obtained upon checking the energy were exactly the same, the value of the energy was printed rather than their difference (zero). Files Added: source/mc/mcmini.src Files Modified: source/mc/mc.src /mcener.src /moveio.src /movead.src /mvdihe.src /fcm/mc.fcm /energy/printe.src /charmm/iniall.src /nbonds/enbond.src /enbondg.src /enbfast.src Modified Documentation: doc/mc.doc ------------------------------------------------------------------------------ 1.3 CHARMMRATE: CHARMM - POLYRATE Interface Name : Jiali Gao, C. Alhambra, J. Corchado, M. L. Sanchez, J. Villa, and D. G. Truhlar Email Address : gao@chem.umn.edu Institution : University of Minnesota Date : December 29, 1999 CHARMMRATE is a module of CHARMM for interfacing it with POLYRATE. The polyrate main program becomes a subprogram of CHARMM. POLYRATE can be called to carry out variational transition state theory calculations with multidimensional semiclassical tunneling contributions. When POLYRATE needs the value or gradient of the potential energy surface, it calls a set of interface routines called hooks. The hooks in turn call CHARMM routines for energies and gradients calculated by molecular mechanics or QM/MM methods. CHARMMRATE-version 1.0 is a module of charmm-version 28 for interfacing it with POLYRATE-version 8.1.1. CHARMMRATE-version 1.0 will be distributed as part of the CHARMM program, beginning with version 28 of CHARMM. The user will also require the CRATE utility for modifying POLYRATE to make it compatible with CHARMM. The prospective user of CHARMMRATE should obtain a valid license for CHARMM and valid licenses for POLYRATE and CRATE from the University of Minnesota (http://comp.chem.umn.edu). Files Added: source/prate/charmmrate.src /fcm/charmmrate.fcm build/UNX/prate.mk Files Modified: source/charmm/charmm_main.src /install.com New Documentation: !! documentation and testcases have not doc/charmmrate.doc !! been completed as of Feb. 10, 2000 !! should be done before c28a3 New Testcases: test/c28test/cr01.inp /cr02.inp test/data/cr01.top /cr01.par /cr02.top /cr02.par ------------------------------------------------------------------------------ 1.4 ACE Enhancement Name : Michael Schaefer Email Address : schaefer@brel.u-strasbg.fr Institution : Univ. Louis Pasteur (Strasbourg) & Harvard Date : Aug 12, 1999 (1) ACE can be used with BLOCK/REPLICA (multiple copies of part of the system) (2) atoms can be fixed (CONS FIX) when using ACE (3) the hydrophobic solvation term of ACE is no longer included in the ELEC energy term (as it should be, since it is non-electrostatic); WARNING: if your analysis of CHARMM log files relies on this, you have to modify your approach! (4) the parameters of the self energy potential of ACE (1/omega, sigma, mue) have been moved to the HEAP, as suggested by B. Broux; this reduces the use of permanent memory significantly, if you compile CHARMM with ACE, but don't use ACE in an application (5) warning messages when using ACE for atom types whose volume has not been assigned in the parameter file; so if you use ACE with conventional param19.inp (w/o volumes), there are lots of warnings; if there are just a few warnings, you have to check whether the atom types concerned are present in the system (6) capability of CHARMM compiled w/o ACE to read parameter files with the volume table added -- this avoids unwanted error messages (7) the HEAP space used by ACE is freed when switching back from ACE to another electrostatic potential (e.g., RDIE) (8) included volume spcification for TIP3P atom types and some comments in the parameter file ./test/data/param19-1.2.inp (9) improved testcase (./test/c27test/ace1.inp) and updated documentation in ./doc/ace.doc Files involved: source/charmm/iniall.src /energy/eutil.src /printe.src /fcm/energy.fcm /inbnd.fcm /io/parmio.src /manip/cstran.src /nbonds/ace.src /acean.src /enbond.src /nbonds.src /nbutil.src test/c27test/ace1.inp /data/param19-1.2.inp doc/ace.doc ------------------------------------------------------------------------------ 1.5 BYCC Modification Name : Robert J. Petrella Email Address : petrella@tammy.harvard.edu Institution : Harvard University Date : December 31, 1999 The only modification involves the removal of the need for cluster files. The algorithm in SUBROUTINE CLSBYRULE clusters the atoms automatically when the MKCLuster (make clusters) command is given. Hence, all the user must do to implement the BYCC algorithm is (1) give the command MKCLusters and (2) specify BYCC in the NBOND command Files Modified: source/nbonds/nbutil.src MKCLUST shortened and CLSBYRULE added /io/rtfio.src RDCLUS removed /mainio.src RDCLUS removed doc/nbonds.doc test/c27test/testbycc1.inp /testbycc2.inp ------------------------------------------------------------------------------ 1.6 TSRI Fixes and Enhancements Name : Charles L. Brooks, III, Michael F. Crowley Email Address : brooks@scripps.edu, crowley@scripps.edu Institution : The Scripps Research Institute Date : January 15, 2000 1.6.1 Compilation Enhancement MPI installation procedures are reworked to modify machine specific Makefiles. Makefile_gnu is modified for pgf compiler and g77 compilation options are added to increase performace by ~100%. The optimization level is altered in nbondg.src compilation for Linux PGI compiler. Files modified: install.com build/UNX/Makefile_cspp /Makefile_gnu /nbonds.mk 1.6.2 Documentation Update Rg/RMSD restraint and Distance Matrix restraint are documnented. File Modified: doc/cons.doc 1.6.3 Memory Save and Bugfixes plnod0 (prnlev node 0) is added and broadcasted to other nodes. Changes are for saving memory, readcv bugfix, initializing variables. A bug is fixed in stream file handling. Files Modified: source/charmm/miscom.src /correl/anacor.src /solana.src /dynamc/dcntrl.src /dynio.src /dynsub.src /trnphi.src /energy/eintern.src /fcm/heap.fcm /parallel.fcm /gener/genpsf.src /image/nbndgcm.src /io/psfres.src /rtfio.src /trajio.src /machdep/paral1.src /manip/corman2.src /cstran.src /dynanal.src /hbanal.src /intcor.src /minmiz/abner.src /misc/hbuild.src (Milan's parallel bugfix) /nmr.src (NO_DQS addded) /sbound.src /nbonds/nbndcc.src /nbonds.src /nbutil.src /pert/block.src /icfcnf.src /rxncor/travel.src /vibran/quasi.src /rbquas.src 1.6.4 Parallel Generalized Born Model Code RMSD-based extension of Rg restraint is added. Parallel gb is fixed and clean up the code. Files Modified: source/energy/energy.src /genborn.src /intere.src /rgy.src /fcm/rgy.fcm 1.6.5 Cray T3E Related Modifications LBYCBIM flag is added in calling parameters. NO_BYCU is fixed. Protected PME_PLAMSA code for non parallel compile. Trajectory format/unformat is fixed. Files Modified: source/nbonds/cenbf.src /nbndgc.src /pme.src /util/util.src 1.6.6 Testcase Fixes Unit number 99 conflicts with an internal file open unit number, changed to 89. And other problems causing crash are fixed Files Modified: test/c20test/dyntest1.inp /quasi.inp /c22test/stdtest.inp /c25test/hba1.inp /c26test/pathint.inp /c27test/mbtest30.inp ------------------------------------------------------------------------------ 1.7 Karolinska Institute Fixes and Enhancements Name : Lennart Nilsson Email Address : Lennart.Nilsson@biosci.ki.se Institution : Karolinska Institute Date : January 31, 2000 1.7.1 Dynamics Restart File Read New option DYNR [CURR|DELT|VEL] added to READ COOR, allowing CURRent coordinates, displcement from current (DELT) coordinates or VELocities to be read from a dynamics restart file. Files new/modified: source/io/coorio.src /dynamc/dynamc.src doc/io.doc test/c28test/dynr.inp: NEW 1.7.2 HEAP Expansion Made HEAP extension working on DEC ALPHA (should also work on other systems with 64 bit pointers, but right now it is implemented under the pref directive ALPHA) File modified: source/machdep/space.src 1.7.3 OS Information Modification of OS information in banner to include number of nodes running the job (from Milan Hodoscek) File modified: source/machdep/startup.src /ctuff.c 1.7.4 Nodenaming Problem Fix Fixed nodenaming problem on parallel setups using the SOCKET library; the original version had an inadvertent wild-card capability making nodenames PE1 and PE10 look identical. Files modified: source/machdep/socket.c 1.7.5 COOR COVA/DMAT File Format Modified output from the COOR COVA and COOR DMAT commands, such that if results are written to a file, as opposed to the charmm output file, all headers and blank lines are skipped. This makes it easier to read the file into a plotting program. Files modified: source/manip/corman2.src 1.7.6 Block Data Fixed block data initialization for the QM interface under GNU (similar as under HPUX) Files modified: source/quantum/qmdata.src /qmset.src 1.7.7 HBOND Analysis Fixed error in calcualtion of average number of hbonds printed for single structure by the COOR HBOND command. Added HBOND DONOR specifications for residue TIP3 in the test topology file. This is needed by the hbanal testcases. File modified: source/manip/hbanal.src test/data/top_all22_prot.inp ------------------------------------------------------------------------------ 1.8 MBO(N)D Updates Name : Masa Watanabe Email Address : watanabe@moldyn.com Institution : Moldyn, Inc. Date : December 23, 1999 1.8.1 MOLDYN Include Files Modifications of MBO(N)D are not correctly implemented in c27b1 and c28a1. The following include files should be located in two places source/fcm and source/moldyn. Both places should have exactly the same files. In c27b1 and c28a1, only source/fcm has the correct version of these files. Copy source/fcm include files into source/moldyn. Files involved: source/moldyn/HANDS2.INC /HEAPMB.INC /IFIRST.INC /INTGRL.INC /PARAM.FOR 1.8.2 MBO(N)D Fixes and Enhancements MBO(N)D related bugs have been fixed and BLAS Library dependent code has been eliminated. MBO(N)D documentation has been updated. c25test/mtsm3.inp is updated to use atom based cutoff. Files modified: build/UNX/Makefile_gnu /Makefile_sgi /Makefile_sgi64 /Makefile_ibmrs source/fcm/mbond.fcm /mbond/mbdiag.src /mbmodes.src /mbond.src /mbutil.src /modtrans.src doc/mbond.doc test/c25test/mtsm3.inp =========================================================================== [2] c28a3 Change Log The following are introduced and modified during the development period of February 15, 2000 through August 15, 2000. 2.1 Oxford Physical and Theoretical Chemistry Lab Developments Name : Ben Webb, and Paul Lyne Email Address : ben@bellatrix.pcl.ox.ac.uk Institution : Physical and Theoretical Chemistry Lab, Oxford, UK Date : July 15, 2000 2.1.1 QM/MM fluctuating charge implementation (FlucQ) The fluctuating charge model (FlucQ) is implemented in CHARMM and extended for QM/MM simulation with GAMESS-US, CADPAC or MOPAC. It is designed primarily for computationally efficient (approx. 10% overhead) modelling of solvent polarisation in hybrid QM/MM systems. Atomic charges are treated as extra degrees of freedom, and are propagated by extended Lagrangian methods during dynamics simulations. Restart and trajectory files are modified when FlucQ code is active, to store the extra charge information. Extra options have been added to the COOR ANAL command, to allow the calculation of a dipole distribution from a trajectory file. The entirety of these changes is activated by the presence of the FLUCQ keyword in pref.dat. Files Added: build/UNX/flucq.mk source/fcm/flucq.fcm /flucq/flucq.src, fluqdyn.src, fluqene.src, fluqqmmm.src Files Modified: source/cff/enbfast_cff.src, enbonda_cff.src /charmm/charmm_main.src, iniall.src /correl/anacor.src, solana.src /dynamc/dcntrl.src, dynamc.src, dynamc4.src, dynamcv.src, dynio.src /energy/enefscal.src, energy.src, eutil.src, intere.src, printe.src /fcm/energy.fcm, param.fcm /gamint/gamini.src /image/eimage.src, images.src, upimag.src, xtlfrq.src /io/parmio.src, trajio.src /manip/scalar.src /mbond/mbdiag.src /mc/mcener.src, mcimge.src /minmiz/abner.src, conjug.src, egrad1.src, nraph.src, powell.src /steepd.src, tndriv.src /misc/hbuild.src /mmff/enbfast_mm.src, enbscalar_mm.src /nbonds/cenbf.src, enbfast.src, enbond.src, enbonda.src, enbondg.src /evdwf.src, ewald.src, grape.src, nbonds.src /pert/epert.src, icfcnf.src, icpert.src, tsme.src /quantum/qmene.src New/Modified Documentation: doc/corman.doc, flucq.doc[New], scalar.doc New/Modified Testcase: test/c28test/fqam1.inp, fqgamess.inp /data/flucq.crd, flucq.gms, flucq.prm, flucq.rtf .............................................................................. 2.1.2 Changes for compilation with Compaq compilers on Alpha Linux A compiler switch (FORT) is added to install.com to build CHARMM (and, if present, CADPAC and GAMESS-US) with the Compaq Fortran and C compilers on Alpha systems running Linux (use it with "./install gnu medium FORT" or similar). CHARMM and GAMESS-US are built with 8-byte integers, for proper functioning of dynamic memory (heap expansion). A new target, "axp-linux", is added to gmscomp, which requires a version of GAMESS-US recent enough to have *ALX cards in unport.src (a patch is available on request). Problems: the assumption that integers are four bytes long is widely spread throughout the CHARMM code; some of these problems have been fixed here (e.g. the RXNCOR code) but the main problem is that PSND4 is used to send both integers and REALs to other nodes, so parallel builds are still broken. In the long term, perhaps an explicit "pointer" type should be added (via. preprocessor, probably) and the PSND4 and PSND8 routines replaced with "send real", "send real*8" and "send integer". Files Modified: install.com build/UNX/Makefile_gnu, gmscomp source/cadint/cadini.src /cadpac/intro.F /fcm/cadpac.fcm /machdep/space.src /rxncor/rxndef.src, rxnene.src .............................................................................. 2.1.3 RXNCOR parallel fixes The RXNCOR code is modified to run certain parts of the code only on node 0, as it expects to access files (e.g. to print the trace file) which is generally possible only on this node. Files Modified: source/energy/energy.src rxncor/rxndef.src .............................................................................. 2.1.4 MMFF with g77 fix A simple one-line fix enables proper compilation of the MMFF code on systems using the g77 Fortran compiler. Files Modified: source/mmff/merckio.src .............................................................................. 2.1.5 CADPAC and QUANTUM fixes, and port to GNU platform A Makefile is provided for building CADPAC on a GNU machine (Intel or Alpha Linux). This requires a modified CADPAC distribution (not distributed with CHARMM) in order to build properly. The install script and Makefile for compilation on SGI platforms has also been fixed for parallel and/or 64-bit installations. Although QUANTUM in c28a2 will compile on GNU platforms, it will not run; a Makefile and modified install script is provided here for its proper functioning. Files Added: build/UNX/cadpac.mk_gnu /quantum.mk_gnu Files Modified: install.com build/UNX/cadpac.mk_sgi source/cadint/cadpac/adapquad.F, angmom.f, atoms.F, banner.f, brueckner.F /chf.f, ddipmpc.f, ddjk.F, dftchf.F, dftmxm2.F /eigen.F, impt.f, index4.F, intro.F, io.F, jkder.F /magdft.F, main.F, master.F, mod2.F, mogues.F /mp2grad.F, mtimit.F, newint.F, nmrs.f, numprop.f /pack.F, paral.F, quadrature.f, scf.F, sorto.f /standv.F, start.F, stvder.F, tdhf.F, utilxx.F /utilyy.f ------------------------------------------------------------------------------ 2.2 Enhancements to the Monte Carlo Module and Bugfixes Name : Aaron R. Dinner Email Address : aaron@bellatrix.pcl.ox.ac.uk Institution : University of Oxford Date : 20 June 2000 2.2.1 MC Enhancements 1) The ACE/ACS solvation energy term is now supported. As described in mc.doc, exact calculation of the screening energy is highly inefficient, and an approximate scheme is introduced to accelerate MC simulations which use this solvation model. 2) It is now possible to minimize the system with the conjugate gradient (CG) algorithm prior to application of the acceptance criterion. CG is specified by the keyword "MINI CONJ" in a MOVE ADD call: MOVE ADD (no mini keywords ) --> no minimization MOVE ADD (NSTEps > 0 ) --> SD minimization MOVE ADD (NSTEps > 0, MINI SD ) --> SD minimization MOVE ADD (NSTEps > 0, MINI CONJ) --> CG minimization MOVE EDIT should work the same way. Several parameters for CG minimization are fixed at their default values (NCGC = 100, PCUT = 0.9999, TOLIter = 100), which could be changed in future versions if there is interest. 3) The INBFrq keyword is now recognized in the MOVE ADD command and controls the non-bond list update during minimization. Note that it is separate from the INBFrq keyword in the MC command. 4) A heuristic non-bond list update has been implemented for MC. The check is done at the end of each -INBFrq moves. The frequencies of image list updates (IMGFrq) and energy checks (IECHeck) need no longer be multiples of INBFrq, but the former will force a non-bond list update. If either of these parameters is negative, the corresponding update will be performed whenever a heuristic non-bond list update is done (and thus should be used only with INBFrq < 0). 5) It is now possible to go through the move set in regular rather than random order. The keyword to toggle this feature is PICK in MC: PICK = 0 (default) Random move group (i.e., a MOVE ADD call) and random move instance within that group. PICK = 1 Sequential move group and sequential move instance within that group. PICK = 2 Random move group and sequential move instance within that group. Note that, for PICK = 2, one does not a priori know how many steps will cover the move set evenly if the numbers of move instances for different move groups is different, so there can be a slight end effect. For example, suppose there are seven steps left and it is time to pick a new group of move instances; if the move group picked has more than seven instances, only the first seven will be tried. Files Added: source/mc/mcace.src Files Modified: source/mc/mc.src, mcener.src, mcmini.src, movead.src, moveio.src /fcm/mc.fcm Modified Documentation: doc/mc.doc .............................................................................. 2.2.2 Bugfixes 1) SKIP NONE SKIP NONE turns off QM electrostatic terms. Correct QEQTRM(I) = SKIP to QEQTRM(I) = SKIPN. Files involved: source/energy/eutil.src 2) QM/MM VDW energy calculations QM/MM VDW energies vary with machine due to failure to update group centers in some cases. A logical variable is passed to an integer argument (LCENTR) of EGROUP, which results in a machine-dependent cast. Files involved: source/quantum/qmene.src 3) Program hangs during first energy calculation GNU preprocessor options concerning QMMMDATA should be the same as ALPHA/IRIS/DEC rather than OS2/HPUX. Local variables are not properly initialized. Add the compiler flag '-finit-local-zero -fno-automatic' to the FC0 macro. Files involved: source/quantum/qmdata.src, quantum/qmset.src build/UNX/Makefile_gnu ------------------------------------------------------------------------------ 2.3 University of Minesota Developments Name : Cristobal Alhambra, J. Corchado, M. L. Sanchez, J. Villa, Jiali Gao and D. G. Truhlar Email Address : alhambra@chem.umn.edu Institution : U. of Minnesta Date : June 26, 2000 2.3.1 CHARMM/POLYRATE interface charmmrate is a module of charmm for interfacing it with polyrate. The polyrate main program becomes a subprogram of charmm. polyrate can be called to carry out variational transition state theory calculations with multidimensional semiclassical tunneling contributions. When polyrate needs the value or gradient of the potential energy surface, it calls a set of interface routines called hooks. The hooks in turn call charmm routines for energies and gradients calculated by molecular mechanics or QM/MM methods. charmmrate-version 1.0 is a module of charmm-version 27 for interfacing it with polyrate-version 8.1.1. charmmrate-version 1.0 will be distributed as part of the charmm program, beginning with version 27 of charmm. The user will also require the crate utility for modifying polyrate to make it compatible with charmm. The prospective user of charmmrate should obtain a valid license for charmm from an authorized charmm licenser and valid licenses for polyrate and crate from the University of Minnesota (http://comp.chem.umn.edu). Files Added: source/prate/charmmrate.src /fcm/charmmrate.fcm build/UNX/prate.mk Files Modified: install.com source/charmm/charmm_main.src New Documentation: doc/charmmrate.doc New Testcase: test/c28test/cr01.inp, cr02.inp test/data/cr01p_ini.crd, cr01r_ini.crd, cr01ts_ini.crd, /cr02.crd, cr02.para, cr02.topo, optcr02.crd .............................................................................. 2.3.2 Semiempirical Valence Bond (SEVB) Term The SEVB term is a correction to the PES when combined semiempirical NDDO QM/MM hamiltonians are used to model the reactivity in enzyme active sites. The code assigns two extended London-Eyring-Polanyi-Sato (LEPS) potentials to the subsystem {A,B,D} mimicking the acceptor, transferred, and donor sites, and the necessary parameters entering in the definition of the Morse functions, i.e. dissociation energies (Dxy), equilibrium distances (Rxy), beta exponents (bxy), and Sato parameters (Sxy). During a molecular dynamics simulation the value of the SEVB energy and gradients are evaluated at every step from the instantaneous configuration of the system and added to the corresponding arrays. Files Added: source/fcm/leps.fcm /quantum/qmleps.src Files Modified: source/quantum/qmset.src, qmene.src Modified Documentation: doc/qmmm.doc New Testcase: test/c28test/testleps.inp ------------------------------------------------------------------------------ 2.4 Biased Molecular Dynamics: Half Quadratic Bias Method (HQBM) Name : Emanuele Paci Email Address : paci@pandora.u-strasbg.fr Institution : Univ. Louis Pasteur (Strasbourg) & Oxford University Date : Jul 15, 2000 Biased molecular dynamics implementation based on a time dependent half quadratic perturbation designed to induce large conformational changes on the simulation timescale and generate low energy pathways. Files Added: source/energy/hqbm.src /fcm/hqbm.fcm Files Modified: source/charmm/charmm_main.src /energy/energy.src /energy/eutil.src /fcm/energy.fcm New Documentation: doc/hqbm.doc New Testcase: test/c28test/hqbm.inp test/data/1aps.crd, 1aps_mini.crd ------------------------------------------------------------------------------ 2.5 Targeted Molecular Dynamics (TMD) Name : Jianpeng Ma Email Address : jma@tammy.harvard.edu Institution : Harvard University Date : July 20, 2000 This is only for TMD using holonomic RMS constraint. For doing Targeted Molecular Dynamics (TMD), one needs to define a moving coordinate and a target coordinate. You slowly pull the moving structure towards the target structure by gradually decreasing the RMS distance between two. The 'pulling' speed is defined by user. Several new keywords for charmm dynamic command (DYNAmic) have been added. To invoke TMD, very similar to Berendsen's constant temperature method, one needs to start with the keyword TARGet, then followed by a few others defined detailed parameters such as the number of atom that subject to TMD constraint (NTAR), number of dynamic steps for stopping artificial rotation (INRT), and RMS increment (DINC). The TMD code can work with and without SHAKE. Files Added: source/dynamc/tmd.src /fcm/tmd.fcm Files Modified: source/charmm/charmm_main.src /dynamc/dcntrl.src, dynamc.src, dynamc4.src, dynio.src /energy/eutil.src /minmiz/minmiz.src Modified Documentation: doc/dynamc.doc New Testcase: test/c28test/tmdtest.inp ------------------------------------------------------------------------------ 2.6 BYCC Enhancements Name : Robert J. Petrella Email Address : petrella@tammy.harvard.edu Institution : Harvard University Date : June 22, 2000 2.6.1 EEF1 Modification Modified eef1 to be compatible with active atom selections (i.e. with NBACtive command used in conjunction with BYCC non-bonded option). Since only active atoms appear in the nonbonded list, the ATOMON array flags (=1) the atoms appearing in the list. Solvation energies are then calculated only with the flagged atoms. Modified Files: source/misc/eef1.src SUBROUTINE EEF1EN, SLVPRINT and EEF1IM /energy/energy.src SUBROUTINE ENERGY /intere.src SUBROUTINE INTER2 doc/eef1.doc .............................................................................. 2.6.2 BYCC code Enhancements Reduced memory requirements of the BYCC option by assigning arrays to temporary memory (stack). Eliminated unnecessary common block variables in actclus.fcm. Also, removed SUBROUTINE RDCLUS from rtfio.src. Modified Files: source/nbonds/nbndcc.src SUBROUTINE NBNDGG /nbonds.src /io/rtfio.src /fcm/actclus.fcm ------------------------------------------------------------------------------ 2.7 Karolinska Institute Fixes and Enhancements Name : Lennart Nilsson Email Address : Lennart.Nilsson@biosci.ki.se Institution : Karolinska Institute Date : July 15, 2000 2.7.1 COOR DMAT A bug in the code for the RMSF option is fixed and the following new keywords are added: MATRix to give output in a matrix format, applies to the distance as well as distance fluctuations RELAtive to give relative distance fluctuations DUNIt to give distance matrix output and fluctuations in one go Files involved: doc/corman.doc source/manip/corman2.src .............................................................................. 2.7.2 COOR COVA The new keyword MATRix is added to give output in matrix format. Files involved: doc/corman.doc source/manip/corman2.src .............................................................................. 2.7.3 COOR HBOND Modifed output format. With keyword VERBose one now gets listing of all pairs of hbonds between atoms in the two selections (previously one would only get statistics for the atoms in the first selection). Files involved: doc/corman.doc source/manip/hbanal.src .............................................................................. 2.7.4 TRAJ READ/WRITe Documentation is clarified. Files involved: doc/dynamc.doc ------------------------------------------------------------------------------ 2.8 TSRI Fixes and Enhancements Name : Charles L. Brooks, III, Michael F. Crowley Email Address : brooks@scripps.edu, crowley@scripps.edu Institution : The Scripps Research Institute Date : July 17, 2000 .............................................................................. 2.8.0 General overview. We have introduced a number of improvements toward making CHARMM functionally more friendly and performance-wise better, these are described in 2.8.1 - 2.8.5. Additional bugfixes for particular machines and algorithms are described in 2.8.6 and 2.8.7. Finally, new developments/improvements for "generalized homology modeling" (see http://mmtsb.scripps.edu), 2.8.8, and lambda-dynamics improvements (including enhancements to allow GB to be used with BLOCK), 2.8.9, are described. .............................................................................. 2.8.1 Fast Shake. This modification involves bring the "fast vector" SHAKE into operation w/ fast scalar commands to utilize the analytic 3x3 water-specific SHAKE algorithm. This should become the default for SHAKE in CHARMM, it improves performance when water rigid molecules are employed very substantially. It is accessed currently as documented in the SHAKE documentation w/ the shake fast option. KEYWORD: FSSHK source/charmm/iniall.src source/dynamc/dcntrl.src source/manip/shake.src .............................................................................. 2.8.2 This modification permits access to both a list and substitution varibles for query regarding the specific pref.dat options used in building a given CHARMM executable. Documentation appears in the misc.doc and subst.doc document files. KEYWORD: PREFMSI source/charmm/iniall.src doc/miscom.doc, subst.doc .............................................................................. 2.8.3 This modification was introduced to make permit easier use of CHARMM on MPI-parallel systems that do not support sdin and stdout. It turns off stdin and stdout and redirects automatically to files charmm.inp and charmm.out respectively. KEYWORD: FILEINPUT KEYWORD: FILEOUTPUT source/machdep/machio.src .............................................................................. 2.8.4 Nested Timers to permit more detailed timing information to be gathered for performance assessment. KEYWORD: NEWTIMER source/charmm/charmm_main.src, iniall.src source/dynamc/dcntrl.src, dynamc.src source/energy/energy.src source/image/nbndgcm.src source/manip/shake.src .............................................................................. 2.8.5 install.com Added "nolog" command option so log file is not created and compile output goes to stdout instead - a useful tool for development. All .mk files changed to enable the "keepf" and "keepo" install.com options. .............................................................................. 2.8.6 Bugfixes for ibmsp machines source/machdep/paral1.src .............................................................................. 2.8.7 Bugfixes for various problems from c28a2. KEYWORD: PMEPLSMA source/mmff/merckio.src source/nbonds/ace.src, enbfast.src, pme.src, pmeutil.src source/quantum/qmpac.src doc/nbonds.doc .............................................................................. 2.8.8 Center of Mass Harmonic Constraints for use in lattice/all atom refinement with "generalized homology modeling" tools being build by M. Feig. KEYWORD: HMCM source/charmm/iniall.src source/energy/ecnstr.src, energy.src, eutil.src, printe.src source/fcm/cnst.fcm, dimens.fcm, energy.fcm source/manip/cstran.src source/pert/epert.src test/c28test/hmcm.inp test/data/pep5.pdb doc/cons.doc .............................................................................. 2.8.9 Improvements and new additions to lambda-dynamics code/methods to permit 1) more general umbrella potentials that are lambda-dependent be applied for improved convergence and sampling during lambda-dynamics (See S. Banba et al., JCP, 2000; JPC, 2000); 2) to allow use of the generalized Born module with the BLOCK and lambda-dynamics approaches. These are developments from Shinichi Banba while at TSRI. NOTE: Some of these keywords will change and be eliminated to more tightly incorporate developments in the next release. KEYWORD: BANBA KEYWORD: LDLAN KEYWORD: LDMGEN KEYWORD: LMC KEYWORD: LRST KEYWORD: GBBLCK KEYWORD: GBFIXAT source/charmm/iniall.src source/dynamc/dcntrl.src, dynamc.src, dynio.src, dynlng.src source/energy/eintern.src, enefscal.src, eutil.src, genborn.src source/fcm/block.fcm, genborn.fcm, lambda.fcm, reawri.fcm, rwlam.fcm source/image/images.src source/nbonds/enbfast.src, enbond.src, enbonda.src, nbutil.src source/pert/block.src test/c28test/GB_block.inp, GB_fep.inp, GB_ldm.inp, GB_mcmd.inp /ldm_lang.inp, ldm_lang_slow.inp, ldm_rst.inp, ldm_rst2.inp /ldm_rst2_slow.inp, ldm_rst_slow.inp /mcmd_rst.inp, mcmd_rst2.inp, mcmd_rst2_slow.inp, mcmd_rst_slow.inp /replica_genborn1.inp, replica_genborn2.inp, replica_genborn3.inp doc/block.doc, dynamc.doc, genborn.doc, pdetail.doc ------------------------------------------------------------------------------ 2.9 Slovenia National Institute of Chemistry Developments Name : Milan Hodoscek Email Address : milan@kihp6.ki.si Institution : National Institute of Chemistry, Slovenia Date : June 23, 2000 2.9.1 Name conflicts resolved Due to GAMESS compatibility problems, - NORM subroutine was changed to TQNORM - EPSLON subroutine was changed to EPSLN - PSETUP subroutine was changed to PRSET - PATH subroutine was changed to PATHC Files modified: source/charmm/charmm_main.src /correl/solana.src /dimb/eispack.src /dynamc/dcntrl.src, prssre.src /rxncor/path.src .............................................................................. 2.9.2 GAMESS code update 1) New GAMESS version (includes DFT) replaces gamint/gamess. Parallel library DDI is partially implemented in CHARMM for better performance. File Added: source/gamint/ddi.src 2) New NOGUess option in GAMEss command added. It speeds up some calculations and make others possible. Default is still the old behavior. Files modified: doc/gamess.doc source/fcm/gamess.fcm /gamint/gamini.src, blur.src test/c25test/gmstst.inp .............................................................................. 2.9.3 Header Enhancement More informational printout in the CHARMM header. It reports the hostname of the machine (and for parallel also number of additional processes) and more specific information of the operating system. Files modified: source/machdep/cstuff.c, startup.src .............................................................................. 2.9.4 Minor Enhancements "Y2K" fix and more precision in timings. Format for Volume calcultations increased. Files modified: source/machdep/cstuff.c, machutil.src /manip/corman2.src ------------------------------------------------------------------------------ 2.10 CHARMM / GAMESS-UK Interface Name : Paul Sherwood Email Address : p.sherwood@daresbury.ac.uk Institution : CLRC Daresbury Lab. Date : July 20, 2000 Ab initio program GAMESS-UK (General Atomic and Molecular Electronic Structure System, UK version) is connected to CHARMM program in a QM/MM method. This method is based on the interface to the GAMESS (US version), the latter being an extension of the QUANTUM code which is described in J. Comp. Chem., Vol. 11, No. 6, 700-733 (1990). Some references are renamed in order to resolve conflics between CHARMM and GAMESS-UK as follows. All other remaining clashes have been resolved by changing GAMESS-UK source. common/equiv => common/equiv0 in fcm/cff.fcm common/deriv => common/derivr in fcm/deriv.fcm function lstchr => lastch in cff/parrdr_cff.src function INLIST => QINLIST in image/nbondm.src, nbonds/nbonda.src, nbonds/nbondg.src, nbonds/nutil.src ortho1 => ortho1p in rxncor/path.src shut => chmshut in machdep/socket.c New Module and Files: source/gukint source/gukint/gukini.src doc/gamess-uk.doc test/c28test/alanine_guk.inp /data/alanine_guk.in Modified Files: install.com build/UNX/Makefile_sgi and Makefile_gnu source/charmm/charmm_main.src, iniall.src /energy/energy.src /gener/update.src /machdep/startup.src /nbonds/nbonda.src, nbonds.src /quantum/addlnat.src Notes: a) sgi and gnu are the only platforms that the code is tested on. b) Corrected logical test in mmff/merckio.src. ------------------------------------------------------------------------------ 2.11 Combination of soft core potentials and PERT Name : Stefan Boresch and Michael Brunsteiner Email Address : stefan@mdy.univie.ac.at Institution : University of Vienna, Austria Date : July 5, 2000 The PERT free energy module of CHARMM is based on a linear dependence on the coupling parameter. While simplifying implementation, this approach is prone to van der Waals endpoint problems. One widely used method to overcome the van der Waals endpoint problem is the use of soft core Lennard Jones and electrostatic interactions for those energy terms that cause problems. This capability has been added, following Zacharias, Straatsma and McCammon, J. Chem. Phys. 1994, 100, 9025. A first publication in which a development version of the code was used is Brunsteiner & Boresch, JCP 2000, 112, 6953-55 Modified Files: source/charmm/iniall.src initialization /energy/enefscal.src force use of slow energy routines in subr. FASTST /nbonds/enbonda.src trap case PSSP; call spec. purpose energy routines /enbondg.src /pert/epert.src bulk of changes, spec. purpose energy routines added /pert.src parsing, initialization, resetting; adding of add. dU/dL contributions to standard array entries /fcm/pert.fcm definitions of nonlocal variables Modified Documentation: doc/pert.doc New/Modified Testcase: test/c28test/pssp1.inp, pssp2.inp, pssp3.inp /data/pssp3.pun ------------------------------------------------------------------------------ 2.12 Cornell University Developments Name : Wonpil Im and Benoit Roux Email Address : Benoit.Roux@med.cornell.edu Institution : Cornell University Date : 5 July, 2000 2.12.1 Generalized solvent boundary potential (GSBP) A generalized solvent boundary potential (GSBP) has been implemented for simulation of a reduced region while incorporating the influence of the surrounding implicitly. GSBP is in the same spirit as the SBOUND potential and the SSBP but is relies heavily on the PBEQ module. The current implementation of the method is described in W. IM, S. Berneche and B. Roux. J. Chem. Phys. (2000, to appear). The GSBP represents the electrostatic forces from the surrounding as the use of 2 components: One is the static external field which comes from the charge distribution in the outer region considering the environment as a featureless dielectric medium. The second one is the reaction field which is created by the charge distribution inside the inner region considering the whole molecular configuration and the solvent. New Files: source/misc/gsbp.src, gsbp2.src Modified Files: install.com (gsbp keyword) source/energy/energy.src, eutil.src, printe.src /misc/pbeq.src, pbeq2.src /fcm/energy.fcm, pbeq.fcm Modified Documentation: doc/pbeq.doc New Testcases: test/c28test/gsbptest1.inp test the setup of the static field and reaction field matrix calculation test/c28test/gsbptest2.inp generate short trajectory with GSBP forces .............................................................................. 2.12.2 Miscelaneous upgrades for the PBEQ module The PBEQ (Poisson-Boltzmann finite-difference solver) has been upgraded and improved. Several methods for solving the finite difference equation have been implemented and tested. Full multi-grid relaxation (FMGR), optimized successive over relaxation (OSOR), 3D periodic boundary conditions. Non-linear and partially linearized PB equation have been implemented. The performance of the code has been tested and improved by comparing with delPhi. The performance is now fairly similar to that of delPhi. A complete benchmark input file pbeqtest6.inp is introduced to test all the convergence methods for a grid of 65 cubic (estimated run time is about 15 minutes on Pentium III). A new stream file pka.str has been introduced to calculate pKa of ionizable residues with all atom PARAM22. The charges of the 2 states are stored in scalar store 1 and store 2. The usage of the stream file is illustrated in the pbeqtest7.inp file. Modified File: source/misc/pbeq.src, pbeq2.src /fcm/pbeq.fcm Modified Documentation: doc/pbeq.doc New Testcases: test/c28test/pbeqtest4.inp test 3D periodic boundary conditions /pbeqtest5.inp test non-linear and partially linearized PB /pbeqtest6.inp benchmark of all the finite-difference solvers /pbeqtest7.inp example of pKa calculation with pka.str test/data/pka.str, rs12_asp1.crd, str1.crd .............................................................................. 2.12.3 Multiple RMSD (BestFit) harmonic restraints A new restraint has been introduced to manipulate and control macromolecular conformations. The new restraint is related to the CONS HARM BestFit, which sets up harmonic restraints with respect of a reference structure. However, because all the reference data structure is stored in XREF, YREF, ZREF, this command allows only a single bestfit restraint. In addition, it allows only a restraint to zero value of RMSD. It is useful to allow multiple such bestfit RMSD restraint to progress from one conformation to a second conformation of a molecular system. The new command CONS RMSD allows such multiple bestfit restraint. The form of the new restraint energy is: E = Sum_i KFORCE_i * [RMSD - OFFSET_i]**2 Where RMSD is the (possibly mass-weighted) root-mean-square-deviation (RMSD) of the current coordinates with respect to a reference structure, KFORCE_i is a force constant, and OFFSET_i is a constant value setting a relative distance with respect to the RMSD of the structure. The restraint energy is equivalent the normal BestFit energy. The forces have been checked with the TEST FIRST command. The syntax is very similar to all current restraints in CHARMM: CONS RMSD {FORCE } {OFFSET } - [mass] [comp] [norotation] [notranslation] atom-selection sets a RMSD new restraint. It should be noted that all the data structure is stored dynamically on the HEAP and thus, no extra permanent (static) storage is introduced. CONS CLEAR removes all multiple RMSD restraints CONS RMSD SHOW prints all current RMSD restraints with all parameters. New Files: source/energy/rmsd.src /fcm/rmsd.fcm Modified Files: source/energy/ecnstr.src /manip/cstran.src Modified Documentation: doc/cons.doc New Testcase: test/c28test/test_rmsd.inp .............................................................................. 2.12.4 Patch RTF generator for PERT calculations A new utility command MKPRES has been introduced to write a PATCH for adding a dummy sidechain onto a backbone with the goal of performing free energy calculations. The command generates the list of needed dihedral angles and non-bonded exclusions. New File: source/gener/mkpres.src Modified File: source/charmm/charmm_main.src Modified Documentation: doc/pert.doc New Testcase: test/c28test/mkpres.inp .............................................................................. 2.12.5 Bugfix: MMFP GEO PLANAR It is possible to set a distance restraint between the center of mass of two atom selection using the GEO restraint. If the keyword planar is used, the restraint applied only for the projection along the planar normal (given by xdir ydir zdir , see doc/mmfp.doc). File Involved: source/misc/mmfp.src ============================================================================== [3] c28a4 Change Log The following are introduced and modified during the development period of August 15, 2000 through February 15, 2001. 3.1 Oxford Physical and Theoretical Chemistry Lab Developments Name : Ben Webb Email Address : ben@bellatrix.pcl.ox.ac.uk Institution : Physical and Theoretical Chemistry Lab, Oxford, UK Date : November 30, 2000 3.1.1 QM/MM fluctuating charge improvements 1) Bugs with freeing memory on shutting down FlucQ, and reading restart files on parallel machines, are fixed. 2) Charge thermostatting is now supported via. Nose-Hoover, coupling to an external heat bath, or simple velocity scaling. This is set up with the FQMASS, FQTCOU and FQSCAL options to the DYNAmics command, respectively. 3) FlucQ simulations are now supported with Ewald (not PME) calculations. 4) An interface to GAMESS-UK is now in place, which requires the standard GAMESS-UK distribution to be suitably patched. 5) Patches for CADPAC, GAMESS-US, and GAMESS-UK are available in support/patch to allow FlucQ to function properly with these packages. Files Modified: source/flucq/flucq.src, fluqdyn.src, fluqqmmm.src /charmm/iniall.src /dynamc/dcntrl.src, dynio.src /energy/energy.src /fcm/flucq.fcm /gukint/gukini.src /nbonds/enbond.src, ewald.src, ewaldf.src Files Added: support/patch/cadpac.patch, gamess-uk.patch, gamess-us.patch New/Modified Documentation: doc/flucq.doc New/Modified Testcase: test/c28test/fqam1.inp, fqguk.inp /data/fq_guk.in .............................................................................. 3.1.2 Changes for proper MPI functioning under Alpha Linux (GNUALPHA) CHARMM must be built with 64-bit integers under Alpha Linux (using the Compaq C and Fortran compilers, by means of the FORT switch to install.com) in order for heap expansion and GAMESS to function correctly. However, external libraries (e.g. for MPI) are generally built with 32-bit integers. Thus, in order for CHARMM to interface properly with these libraries, all integer arguments must be explicitly passed as INTEGER*4. Routines that assume integers to be 4 bytes in length must also be changed to use 8 bytes. The implementation for MPI under Alpha Linux has been tested for CHARMM linked with the MPICH libraries (also compiled with Compaq's ccc/fort) on a network of EV56 machines. install.com has also been modified to force mpif.h to explicitly define integers as INTEGER*4 under Alpha Linux. install.com now also uses mpicc/mpif77 rather than gcc/g77 on all GNU systems when MPI is requested. Files Modified: install.com source/machdep/paral1.src, paral2.src, paral3.src /gamint/ddi.src .............................................................................. 3.1.3 Addition of PM3 parameters to QUANTUM PM3 parameters are added to the existing AM1 and MNDO parameters for QUANTUM. They can be used by specifying the 'PM3' option to the QUANTUM command rather than 'AM1'. Also, by default QUANTUM uses the CHARMM nonbond cutoffs for the QM/MM interaction (this differs from GAMESS/CADPAC, which interact with all MM atoms). This behaviour can be disabled, such that QUANTUM interacts with all MM atoms, by giving the 'NOCUtoff' option to the QUANTUM command. Files Modified: source/fcm/quantm.fcm, am1parm.fcm /quantum/qmdata.src, qmene.src, qmpac.src, qmset.src, qmnbnd.src New/Modified Documentation: doc/qmmm.doc New/Modified Testcase: test/c28test/pm3.inp .............................................................................. 3.1.4 Addition of a "simple combination" to RXNCOR code The existing RXNCOR "COMBination" command is supplemented by a "simple" combination ("SCOMbination") command. This takes a simple weighted sum of all names, as opposed to a weighted mean, and thus allows negative weights for tracing (for example) the difference between two bond lengths. Files Modified: source/rxncor/rxndef.src New/Modified Documentation: doc/umbrel.doc ------------------------------------------------------------------------------ 3.2 University of Minesota Developments Name : Jiali Gao Email Address : gao@chem.umn.edu Institution : University of Minnesota Date : December 29, 2000 3.2.1 Semiempirical Quantum-Molecular Mechanical Code Enhancements 1) QM/MM electrostatic free energy perturbation A new option is added to the QUANtum command to perform free energy calculations for QM/MM interactions. The PERT command performs electrostatic free energy decoupling calculations for QM/MM interactions on the fly of a molecular dynamics simulation. The algorithm is based on a method described in J. Gao, J. Phys. Chem. 96, 537 (1992). Through a series of simulations, the electrostatic component of the free energy of solvation can be determined. 2) QM/MM interaction energy decomposition The DECOmposition option is added to the QUANtum commad, which initiates an qm/mm interaction energy decomposition calculation on the fly during a molecular dynamics simulation using the QUANtum command. It is currently implemented only for semiempirical Hamiltonians. The analysis is based on the method reported in J. Gao and X. Xia, Science, 258, 631 (1992). It decomposes the total QM/MM electrostatic interaction energy into a vertical interaction energy Evert, and a polarization term Epol. The latter is further separated into electrostatic stabilization Estab, and charge distortion Edist. 3) Modification of space allocation for qm/mm interactions Reduce the space allocated for qm/mm interactions. Previously, space for all mm atoms are allocated. Now, it is reduced to only request space for atoms that actual interact with qm atoms. This only affects the semiempirical code. Files Modified: source/quantum/qmene.src, qmnbnd.src, qmset.src /dynamc/dynamc.src /energy/eutil.src Modified Documentation: doc/quantum.doc New Testcase: test/c28test/qmlep.inp Note that qmfep.inp is basically the same input for the qmmm testcase c22test/quantum1.inp .............................................................................. 3.2.2 Umbrella Sampling Free Energy Calculation A biasing potential for umbrella sampling free energy calculations (form 5) is added. RXNCord: UMBRella FORM form KUMB ku DEL0 del0 form functional form of potential ---- ---------------------------- 1 ku*(delta-del0)**2 5 ku*(delta-del0)**2 + Ubias(delta) Ubias is a biasing potential, used in addition to the harmonic restraining potential, to truncate high barriers of activated processes. Ideally, Ubias(Rc) would be the negative of the potential of mean force g(Rc), where Rc is the reaction coordinate. Ubias is implemented as a cubic spline function based on a tabulated data to be read prior to the call of RXNC. Files Modified: source/rxncor/rxndef.src, rxnene.src Modified Documentation: doc/umbrel.doc ------------------------------------------------------------------------------ 3.3 Enhancements to the Monte Carlo Module Name : Aaron R. Dinner Email Address : aaron@bellatrix.pcl.ox.ac.uk Institution : University of Oxford Date : 30 November 2000 1) Hybrid Monte Carlo (HMC) moves were added. In such moves, the positions of the atoms are propagated with a molecular dynamics integrator (DYNAMC). See mc.doc and references therein for further description. 2) Rigid body translations and rotations of heavy atoms and their associated hydrogen atoms (RTRN/RROT BYHEavy) were added. Such moves allow one to compare MC simulations with dynamics simulations constrained with SHAKE BONH directly. For consistency, the CART key word was changed to RTRN BYATom; the subroutines MVRTRN and MVCART were combined to condense the code. 3) Group-based energy calculations now scale correctly with system size. This modification involved changing the calling arguments of EGROUP, ENBFSG, ENBFVG, and EIMNBD, which affected several source files (detailed below). 4) Concerted rotations that select the original conformation (to maintain detailed balance) are now counted as rejections for ARM, DOMC, and MCSTAT. Also, the correct original driver angle rotation is now passed back. Both these changes should improve automatic optimization of CROT moves. 5) The calling arguments of EEF1EN were changed to accelerate MC calculations using this solvation term and for consistency with the group-based energy calculation changes described above. Also, the call to EEF1EN in MCENER was fixed to include the ATOMON list. 6) The LCENTR flag is now handled correctly in ENBFVG. Files Added: mc/mvhmc.src (1) Files Modified: source/dynamc/dynamc.src (1) /energy/energy.src (3,5), intere.src (5) /image/eimage.src (3) /mc/mc.src (1,2,3,4), mcace.src (3), mcener.src (3,5) /mcimge.src (3), movead.src (1,2), moveio.src (1) /mvcrot.src (4), mvrtrn.src (2) /misc/eef1.src (5) /nbonds/enbfast.src (3,6), enbond.src (3), enbondg.src (3) /pert/epert.src (3) /fcm/reawri.fcm (1) Modified Documentation: doc/mc.doc ------------------------------------------------------------------------------ 3.4 TSRI Fixes and Enhancements Name : Charles L. Brooks, III and Michael F. Crowley Email Address : brooks@scripps.edu, crowley@scripps.edu Institution : The Scripps Research Institute Date : December 29, 2000 3.4.1 Installation Enhancements gukint is added to make. ibmsp3 Makefile is added. NOLOG argument is added to send compile output to stdout rather than a log file. Files Added/Modified: install.com build/UNX/Makefile_ibmsp3 [New] .............................................................................. 3.4.2 Grid based energy calculation A new function is added to calculate grid-based energies. Files Modified: source/charmm/charmm_main.src, iniall.src /energy/energy.src, eutil.src, intere.src, printe.src /fcm/energy.fcm, grid.fcm [New], pbeq.fcm /misc/grid.src [New], pbeq.src, pbeq2.src New Documentation: doc/grid.doc .............................................................................. 3.4.3 Timing Calls The new timer function is extended and runs on parallel machines. Files Modified; source/dynamc/dcntrl.src, dynamc.src, dynamc4.src, dynamvv.src /energy/energy.src /util/new_timer.src /fcm/new_time.fcm, parallel.fcm /image/nbndgcm.src /machdep/machio.src, paral1.src, paral2.src, paral3.src /nbonds/enbond.src, ewaldf.src, heurist.src .............................................................................. 3.4.4 Fast SHAKE Fast shake (analytical) for all 2, 3, and 4 body constraints. Set up for all bonh (TIP3, ch, ch2, ch3, nh, etc), Very much improved fast shake for non-vector machines. Works for parallel. (keyword FSSHK) Files Modified: source/fcm/fstshk.fcm /gener/update.src /manip/fsshake.src, shake.src .............................................................................. 3.4.5 Bugfixes and Enhancements doc/cons.doc - insignificant change concerning fast shake /galgor.doc - update for bugfix source/fcm/cff.fcm - ##IF CFF added to save huge amounts of memory when CFF keyword is not used /fcm/dimens.fcm - increased maximum for number of dihedrals for LARGE /fcm/galgor.fcm - changes for ic seed atom specifications /gukint/ukini.src - added ##IF GAMESSUK /io/parmio.src - added ability to have geometric combining rules for vdw parameters enabling OPLS FF to be implemented in charmm (keyword: GEOMVDW) /misc/genetic.src - changes for ic seed atom specifications /mmff/enbfast_mm.src - flucq error fixed: removed offending endif /nbonds/nbexcl.src - makitc_clr() routine added to clear image memory /nbonds/nbonds.src - NO_BYCC logic added /nbonds/nbutil.src - bugfix for softvdw /pert/block.src - fixed allocation of ibvcrrt /util/prpref.src - added FLUCQ .............................................................................. 3.4.5 Testing Lots of test cases changed to fit the formula of being able to stream, get rid of references to unit 5 and unit 99. Check keywords to decide if the test case is appropriate for the pref.dat keywords that were used for the executable being tested. Made run parallel jobs on mpi, t3e, ibmsp3, and ibmsp. Files New/Modified: test/test.com /stream.inp [New] ------------------------------------------------------------------------------ 3.5 Slovenia National Institute of Chemistry Developments Name : Milan Hodoscek Email Address : milan@kihp6.ki.si Institution : National Institute of Chemistry, Slovenia Date : December 28, 2000 3.5.1 EEF1 method is parallelized Files Modified: source/misc/eef1.src Modified Documentation: doc/parallel.doc .............................................................................. 3.5.2 Arrays references Some arrays in common are used in too large loops, and some access the zeroth element, etc.... Files Modified: source/energy/eutil.src - line 388: should be DO I=1,LENENP /io/rtfio.src - line 263: rtrtyp(nrtrs); but nrtrs is put to 0 /util/matrix.src - lines 90,245,285,377,822,1018,1058: A(1) -> A(*) changes /util/title.src - lines 57,59: limit problems in LINE() .............................................................................. 3.5.3 Energy printout with QM/MM QM energies are converted from Hartrees to kcal/mole and become very large numbers which energy/printe.src couldn't handle. Fixed! File Modified: source/energy/printe.src .............................................................................. 3.5.4 Common block names Some of the names in .fcm SAVE statements and COMMON statements don't agree. All such occurences are fixed. Files Modified: source/fcm/fft.fcm /fcm/intcr.fcm /fcm/mmff.fcm .............................................................................. 3.5.5 XXLARGE size keyword install.com xxlarge didn't work. Fixed. Files Modified: install.com source/fcm/heap.fcm /fcm/stack.fcm .............................................................................. 3.5.6 Performance problem Some of the common blocks are not aligned for efficient performance. The speed of CHARMM runs varies if compiled with different pref.dat keywords. File Mofdified: source/fcm/lambda.fcm .............................................................................. 3.5.7 Miscellaneous small bug fixes Files Modifed: source/fcm/lobos.fcm - wrong position of ##ENDIF /gamint/ddi.src - typo in comment statement /gamint/gamini.src - correct message for blur method /image/nbndgcm.src - line 644: xw(3,nat) must go away! /machdep/startup.src - line 229: allow use of parameters for any parallel /manip/shake.src - line 271: call parptupdate() should be removed! /mmff/enbfast_mm.src - line 81: This ENDIF must be deleted! /nbonds/pme.src - line 357: latm problem in parallel install.com - changed: reduced -> reduce as it is in dimens.fcm Modified Documentation: doc/gamess.doc - minor corrections ------------------------------------------------------------------------------ 3.6 Encapsulation of the PERT/PSSP (Soft Core) Code Name : Stefan Boresch Email Address : stefan@mdy.univie.ac.at Institution : University of Vienna, Austria Date : December 17, 2000 The PSSP code (combination of PERT with soft core potentials) added in c28a3 has been put in ##IF PSSP brackets so that it can be cleanly eliminated if not needed. Removing PERT from pref.dat has the same effect (PSSP without PERT is useless). No functional changes were introduced! PSSP is needed in the pref.dat to activate the PERT/PSSP code. Files Modified: source/charmm/iniall.src /energy/enefscal.src /fcm/pert.fcm /pert/epert.src, pert.src ------------------------------------------------------------------------------ 3.7 New Random Number Generator Name : Xiaoliang Qian, Dan Strahs and Tamar Schlick Email Address : qian@biomath.nyu.edu Institution : New York University Date : December 22, 2000 A new Random number generator (RNG) is provided based on Pierre L'Ecuyer & Terry H Andres' C version code (see clcg.src). This RNG combines 4 linear congruential generators (LCGs) to get the long period of about 2^121 for the resulting sequence. Multiple independent streams can also be achieved for parallel computing. The current state for each stream is stored by four integers rather than one for the old RNG. A representative usage of the CLCG RNG and the replacement of the old RNG is needed for MD with the LN integrator, which makes larger systems and longer simulation durations accessible, exhausting the period of the old RNG. To conform to the existing function calling interface, the new RNG accepts a variable ISEED. However, the new RNG actually requires the propagation of four previous states, not just one state; hence, ISEED is now interpreted to select one of several random number streams, ranging from 1 to . (Maxgen is defined in fcm/clcg.fcm). Since ISEED is used to access a particular stream, the default value of ISEED (in iniall.src) will be 1 rather than 314159. Call from subroutines attempting to specify ISEED are reinterpreted as modulo(Maxgen) to select a the random number stream. Note that a separate subroutine SetSeed (clcg.src) is included for setting the initial seed of the new RNGs. The new RND code is activated with the pref key "NEWRNG". The default is still the "old" RNG. Old dynamics restart files are not compatible with the new RNG code. (see dynamc/dynio.src) Multiple streams requires the propagation of 4*Nstream seeds through restart files, where Nstream is the number of streams. This suggests that the fixed format of the restart file would become variable. A possible solution emerges with adding an extra line or variable indicating the number of streams and, hence, the number of seed lines expected to be read. Files Added: source/util/clcg.src /fcm/clcg.fcm Files Modified: source/charmm/iniall.src /util/random.src /dynamc/dynio.src ============================================================================== [4] c28b1 Change Log The following are introduced and modified during the development period of February 15, 2001 through July 15, 2001. c28b0 is the pre-release version tested prior the c28b1 release on August 15, 2001. 4.1 TSRI Fixes and Enhancements Name : Charles L. Brooks, III and Michael F. Crowley Email Address : brooks@scripps.edu, crowley@scripps.edu Institution : The Scripps Research Institute Date : July 2, 2001 4.1.1 install.com Pref keys GBMF, GRID and RCFFT are added. Note that RCFFT works only with PARALLEL. SCALI MPI installation is added and SP3 FSSCK keyword error is fixed. 4.1.2 Genborn Added new GB module to allow individual atom-type based parameterization of Still-like GB model. Still under development. Files modified: doc/genborn.doc source/charmm/charmm_main.src /energy/energy.src, genborn.src, intere.src /fcm/genborn.fcm /machdep/cstuff.c 4.1.3 No Buffering Added keyword to eliminate output buffering. Files modified: source/machdep/cstuff.c 4.1.4 Grid-Based Potentials Additional development of grid-based potentials for ligand-receptor docking studies. Modifications and testcases added. Files modified: source/charmm/iniall.src /energy/energy.src, intere.src /misc/genetic.src, grid.src /util/prpref.src New testcases: test/c28test/gridtest.inp, grid_2.inp /data/3ptb_complex19.crd, 3ptb_complex19.psf, grid_3ptb.bin 4.1.5 Real-to-Complex FFT for PME Using real_to_complex FFT method uses the symmetry of the transformed charge matrix to cut memory requirements in about 1/2 and computation down by about 1/3 or more. Only parallel implementation at present. Speedup of 50% on the FFTs results in 5% overall speedup for dhfr benchmark. pref.dat keyword: RCFFT Files modified: source/nbonds/nbutil.src, pme.src, pmeutil.src 4.1.6 Faster Direct Sum Rearranged loops, moving if statements outside loops (amounts to the same thing as expand) and prescreening the atoms inside the cutoff before doing the 6/12 and erfc loop. pref.dat keyword: FASTEW Files modified: source/nbonds/ewald.src 4.1.7 IEEE 64 Bit Trajectory Reading This is to read t3e/j90 trajectories from SGIs. pref.dat keyword: T3ETRAJ Files modified: source/dynamc/dynio.src /fcm/stream.fcm /util/title.src 4.1.8 Compilation Compilation feature for F90 and N32 added for SGIs pref.dat keyword: SGIF90 Files modified: install.com source/machdep/machio.src, machutil.src, paral2.src, paral3.src /mmff/datastruc.src 4.1.9 test.com Testcases made run on parallel platforms. Need to change file names into lower case only. Also added checking features compiled. Files modified: test/test.com /c20test/brbtest.inp, dyntest2.inp, maatest.inp, trnphi.inp, /vibpafl.inp, vibran.inp, vibwat.inp, vibrtst.inp /c22test/cortst.inp, icfix.inp, icpert.inp, mewtest.inp, /path.inp, pert.inp, slowgr.inp, stdtest.inp, window.inp /c23test/clustst.inp /c24test/pert2.inp /c25test/cortst25.inp, helix.inp, pull.inp, quiet.inp, resdtest.inp, /vibwat25.inp /c27test/cubesgb.inp, genborn19.inp /c28test/alanine_guk.inp, cr01.inp, cr02.inp Files renamed: test/c24test/dyn4dtest.inp /c27test/gb_cff-data.inp, gb_cff95_na-test.inp, gb_cff95_prot-test.inp, /gb_mmff94_na-test.inp, gb_mmff94_prot-test.inp, /gb_mmff94_test.inp /c28test/gb_block.inp, gb_fep.inp, gb_ldm.inp, gb_mcmd.inp ------------------------------------------------------------------------------ 4.2 University of Minesota Developments Name : Jiali Gao Email Address : gao@chem.umn.edu Institution : University of Minnesota Date : June 21, 2001 (1) allowing qm/mm group-group list for mm-group and qm-molecule interactions in qm/mm calculations. (2) efficient management of memory allocation for qm/mm. (3) Inclusion of qm/mm periodic bondary conditions for qm/mm calculations using Charlie Brooks' PBound. Files Modified: source/fcm/nbndqm.fcm /quantum/qmene.src, qmnbnd.src ------------------------------------------------------------------------------ 4.3 CFF Enhancements Name : Nan-Jie Deng Email Address : ndeng@msi.com Institution : Molecular Simulations Inc. Date : April 20, 2001 Second derivatives related bugs/problems in CFF have been fixed and CFF documentation has been updated. This bugfix involves fixing the calculation of analytical second derivatives in the CFF force field. As a result, methods that uses analytical second derivatives such as Newton-Raphson minimization and normal modes calculation are now supported with the use of CFF force field. Files modified: source/fcm/cff.fcm /cff/codes_cff.src, efscalar_cff.src, enbfast_cff.src, /enbonda_cff.src, escalar_cff.src, parrdr_cff.src /charmm/iniall.src /util/parse.src /io/rtfio.src doc/cff.doc ------------------------------------------------------------------------------ 4.4 Harvard University Developments Name : Robert J. Petrella Email Address : petrella@tammy.harvard.edu Institution : Harvard University Date : June 21, 2001 4.4.1 ESTATS Command "ESTATS"-- utility for calculating average and standard deviation of the potential energy and its components "on-the-fly"-- i.e. during the actual simulation or sampling run, without the need for post-processing of trajectory files. pref.dat keyword: ESTATS Files modified: doc/energy.doc source/charmm/charmm_main.src, iniall.src /energy/anal.src, energy.src Files added: source/fcm/estats.fcm 4.4.2 ADUMB Modifications "CORR" keyword--facility for "on-the-fly" calculation of the average values of specified variables as a function of the reaction coordinates in adaptive umbrella sampling runs. Files modified: doc/adumb.doc source/adumb/cmds.src /umb.src /charmm/iniall.src Files added: source/fcm/umbcor.fcm 4.4.3 TSM modifications "RUNA" keyword, used in conjunction with "SAVIc" keyword-- facility for "on-the-fly" calculation of the free energy and average energy values during internal coordinate perturbation. Files modified: doc/perturb.doc source/charmm/iniall.src /fcm/icpert.fcm /pert/tsms.src, icpert.src ------------------------------------------------------------------------------ 4.5 Graphics Module Enhancement Name : Rick Venable Email Address : Rick_Venable@nih.gov Institution : FDA/CBER Biophysics Lab Date : July 16, 2001 4.5.1 Added TRAJ commands to GRAPHX Historically, only "COOR READ ... IFILE n" could be used within GRAPHX to read trajectory frames. Support for TRAJ READ greatly facilitates viewing trajectories or making molecular animations at other than the default SKIP value from the trajectory file. Files Modified: source/graphics/graphx.src doc/graphx.doc ------------------------------------------------------------------------------ 4.6 Bug Fixes and Enhancements Name : Milan Hodoscek Email Address : milan@cmm.ki.si, milan@helix.nih.gov Institution : National Institute of Chemistry, Slovenia Date : July 16, 2001 4.6.1 Added support for MD-GRAPE-II board The new version of GRAPE, which is 10 times faster then previuos versionis now supported. Files Modified: source/charmm/iniall.src /nbonds/enbond.src, grape.src, nbutils.src /fcm/grape.fcm 4.6.2 Compiler fixes - Complaints about the standard routine names SETUP, MERGE - preflx keyword missing Files Modified: source/mmff/mmff.src (SETUP -> SETUPMF) /dynamc/dynsub.src (MERGE -> TMERGE) /charmm/charmm_main.src (MERGE -> TMERGE) /fcm/noe.fcm (!##PNOE missing) 4.6.3 Bug Fixes RGYR command didn't pass TEST FIRSt MINI CONJ fails to converge - bug fixed Files Modified: source/energy/rgy.src (RGYR fix) /minmiz/conjug.src (MINI CONJ fix) 4.6.4 Documentation updated Files Modified: doc/parallel.doc, gamess.doc, developer.doc ============================================================================== [5] c28b2 Change Log The following are introduced and modified during the development period of August 15, 2001 through February 15, 2002. 5.1 TSRI Fixes and Enhancements Name : Mike Crowley, Charles Brooks Email Address : crowley@scripps.edu, brooks@scripps.edu Institution : TSRI Date : December 27, 2001 (1) Added OPLS-AA protein force field to CHARMM. Pref keyword: OPLS Files modified: install.com source/charmm/iniall.src /energy/enefscal.src /util/prpref.src (2) Cray Binary File Read Modified traj read to permit reading Cray binary files on other machines. Pref keyword: T3ETRAJ Files modified: source/dynamc/dynio.src (3) Zero Length Message Changes to eliminate communication of zero length messages. Files modified: source/machdep/paral3.src (4) Fixed IO control in solana Files modified: correl/solana.src (5) Fixed code for parallel compile Files modified: image/nbndgcm.src (6) Code modifications for serial compile with RCFFT Pref keyword: RCFFT Files modified: install.com source/nbonds/pmeutil.src ------------------------------------------------------------------------------ 2.7 Bugfixes (1) Velocity Verlet Restart Name : Arjan van der Vaart Email Address : arjan@schubert.u-strasbg.fr Institution : ISIS Date : November 8, 2001 Restart runs using the velocity Verlet integrator always give SHAKE errors, when heavy atoms bound to the SHAKE-able hydrogens are fixed. File fixed: source/dynamc/dynamvv.src .............................................................................. (2) Parallel EEF1 Fix Name : Arjan van der Vaart Email Address : arjan@schubert.u-strasbg.fr Institution : ISIS Date : December 5, 2001 The parallel implementation of EEF1 gives wrong solvation (and total) energies if more than one processor is used (forces are fine). (Note that the "dirty trick" comments have been deleted, since the "dirty trick" has been replaced by new code) File fixed: source/misc/eef1.src