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