[gmx-users] Re: gmx-users Digest, Vol 99, Issue 79
radhika jaswal
jaswalradhika at yahoo.co.in
Sat Jul 21 07:44:03 CEST 2012
--- On Fri, 20/7/12, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org> wrote:
> From: gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
> Subject: gmx-users Digest, Vol 99, Issue 79
> To: gmx-users at gromacs.org
> Date: Friday, 20 July, 2012, 7:09 PM
> Send gmx-users mailing list
> submissions to
> gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help'
> to
> gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more
> specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Please help with all-angles constraint
> ption (radhika jaswal)
> 2. Re: Please help with all-angles
> constraint ption (Justin Lemkul)
> 3. CHARMM36 - Smaller Area per lipid for
> POPE - Why? (Sebastien Cote)
> 4. is NOASSEMBLYLOOPS broken? (francesco
> oteri)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 20 Jul 2012 18:46:03 +0800 (SGT)
> From: radhika jaswal <jaswalradhika at yahoo.co.in>
> Subject: [gmx-users] Please help with all-angles constraint
> ption
> To: gmx-users at gromacs.org
> Message-ID:
> <1342781163.38035.YahooMailClassic at web193204.mail.sg3.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Dear all,
>
> I did NVT simulations of a number of molecules with double
> bond. But when i analysed the results i realised that double
> bond has been converted to single bond and sp2 hybridisation
> has also changed to sp3. I was doing with all bonds
> constraint option. But when i started with all angles
> constraint option it kept on processing on version 3.3.1
> and with many fatal errors on version 4.5.4.
> I am doing with version 4.5.4 now and pasting the
> parameters i am using and the errors...
> the .mdp file
>
>
> title = nval in energy minimisation after solvating
> cpp = /usr/bin/cpp
> define = -DFLEXIBLE
> constraints = all-angles
> constraint_algorithm = lincs
> lincs_order = 6
> lincs_iter = 1
> integrator = steep
> dt = 0.001 ; ps
> nsteps = 400
> nstlist = 6
> ns_type = grid
> rlist = 0.8
> coulombtype = PME
> rcoulomb = 0.8
> rvdw = 0.8
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ;
> ; Energy Minimizing stuff
> ;
> emtol = 1000.0
> emstep = 0.01
>
> and errors
> /usr/local/gromacs/bin/mdrun -nice 0 -v -s
> nmab2_md_water_em.tpr -c nmab2_md_water_em.gro -g
> nmab2_md_water_em.log -o nmab2_md_water_em.trr -e
> nmab2_md_water_em.edr
>
> :-) G R O M
> A C S (-:
>
> Glycine
> aRginine prOline Methionine Alanine Cystine Serine
>
>
> :-) VERSION
> 4.5.4 (-:
>
> Written by Emile Apol, Rossen
> Apostolov, Herman J.C. Berendsen,
> Aldert van Buuren, Pär Bjelkmar, Rudi
> van Drunen, Anton Feenstra,
> Gerrit Groenhof, Peter Kasson,
> Per Larsson, Pieter Meulenhoff,
> Teemu Murtola,
> Szilard Pall, Sander Pronk, Roland Schulz,
>
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
>
> Berk Hess, David van der Spoel, and Erik
> Lindahl.
>
> Copyright (c) 1991-2000,
> University of Groningen, The Netherlands.
> Copyright (c)
> 2001-2010, The GROMACS development team at
> Uppsala University & The
> Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> This program is free
> software; you can redistribute it and/or
> modify it under the terms
> of the GNU General Public License
> as published by the
> Free Software Foundation; either version 2
> of the
> License, or (at your option) any later version.
>
>
> :-)
> /usr/local/gromacs/bin/mdrun (-:
>
> Option Filename Type
> Description
> ------------------------------------------------------------
> -s nmab2_md_water_em.tpr Input
> Run input file: tpr tpb tpa
> -o nmab2_md_water_em.trr Output
> Full precision trajectory: trr trj
>
>
> cpt
> -x traj.xtc
> Output, Opt. Compressed trajectory (portable xdr format)
> -cpi state.cpt Input, Opt.
> Checkpoint file
> -cpo state.cpt Output, Opt.
> Checkpoint file
> -c nmab2_md_water_em.gro Output
> Structure file: gro g96 pdb etc.
> -e nmab2_md_water_em.edr Output
> Energy file
> -g nmab2_md_water_em.log Output
> Log file
> -dhdl dhdl.xvg Output, Opt.
> xvgr/xmgr file
> -field field.xvg Output, Opt. xvgr/xmgr
> file
> -table table.xvg Input, Opt.
> xvgr/xmgr file
> -tablep tablep.xvg Input, Opt. xvgr/xmgr
> file
> -tableb table.xvg Input, Opt.
> xvgr/xmgr file
> -rerun rerun.xtc Input, Opt.
> Trajectory: xtc trr trj gro g96 pdb cpt
> -tpi tpi.xvg Output, Opt.
> xvgr/xmgr file
> -tpid tpidist.xvg Output, Opt.
> xvgr/xmgr file
> -ei sam.edi Input,
> Opt. ED sampling input
> -eo sam.edo Output, Opt.
> ED sampling output
> -j wham.gct
> Input, Opt. General coupling stuff
> -jo bam.gct Output, Opt.
> General coupling stuff
> -ffout gct.xvg Output, Opt.
> xvgr/xmgr file
> -devout deviatie.xvg Output, Opt.
> xvgr/xmgr file
> -runav runaver.xvg Output, Opt. xvgr/xmgr file
> -px pullx.xvg Output, Opt.
> xvgr/xmgr file
> -pf pullf.xvg Output, Opt.
> xvgr/xmgr file
> -mtx nm.mtx
> Output, Opt. Hessian matrix
> -dn dipole.ndx Output, Opt.
> Index file
> -multidir rundir Input, Opt., Mult. Run
> directory
>
> Option
> Type Value Description
> ------------------------------------------------------
> -[no]h
> bool no
> Print help info and quit
> -[no]version bool no
> Print version info and quit
> -nice int 0
> Set the nicelevel
> -deffnm string
> Set the default filename for all file
> options
> -xvg
> enum xmgrace xvg
> plot formatting: xmgrace, xmgr or none
> -[no]pd bool no
> Use particle decompostion
> -dd vector 0 0
> 0 Domain decomposition grid, 0 is optimize
> -nt int
> 0 Number of threads to start
> (0 is guess)
> -npme int -1
> Number of separate nodes to be used for PME,
> -1
>
> is guess
> -ddorder
> enum interleave DD
> node order: interleave, pp_pme or cartesian
> -[no]ddcheck bool yes
> Check for all bonded interactions with DD
> -rdd
> real 0
> The maximum distance for bonded
> interactions with
>
> DD (nm), 0 is
> determine from initial coordinates
> -rcon
> real 0
> Maximum distance for P-LINCS (nm), 0 is
> estimate
> -dlb
> enum auto
> Dynamic load balancing (with DD): auto, no or yes
> -dds
> real 0.8
> Minimum allowed dlb scaling of the DD cell
> size
> -gcom int -1
> Global communication frequency
> -[no]v
> bool yes
> Be loud and noisy
> -[no]compact bool yes
> Write a compact log file
> -[no]seppot bool no
> Write separate V and dVdl terms for each
>
> interaction type
> and node to the log file(s)
> -pforce real -1
> Print all forces larger than this (kJ/mol nm)
> -[no]reprod bool no
> Try to avoid optimizations that affect binary
>
> reproducibility
> -cpt
> real 15
> Checkpoint interval (minutes)
> -[no]cpnum bool no
> Keep and number checkpoint files
> -[no]append bool yes
> Append to previous output files when
> continuing
>
> from checkpoint
> instead of adding the simulation
>
> part number to all
> file names
> -maxh
> real -1 Terminate after
> 0.99 times this time (hours)
> -multi int
> 0 Do multiple simulations in
> parallel
> -replex int 0
> Attempt replica exchange every # steps
> -reseed int -1
> Seed for replica exchange, -1 is generate a seed
> -[no]ionize bool no
> Do a simulation including the effect of an X-Ray
>
> bombardment on
> your system
>
>
> Back Off! I just backed up nmab2_md_water_em.log to
> ./#nmab2_md_water_em.log.15#
> Getting Loaded...
> Reading file nmab2_md_water_em.tpr, VERSION 4.5.4 (single
> precision)
> Starting 8 threads
> Loaded with Money
>
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.4
> Source code file: domdec.c, line: 6436
>
> Fatal error:
> There is no domain decomposition for 8 nodes that is
> compatible with the given box and a minimum cell size of
> 1.69222 nm
> Change the number of nodes or mdrun option -rcon or your
> LINCS settings
> Look in the log file for details on the domain
> decomposition
> For more information and tips for troubleshooting, please
> check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "Good Music Saves your Soul" (Lemmy)
>
>
> Thanks for all suggestions in advance.
>
> Radhika
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 20 Jul 2012 07:06:37 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Please help with all-angles
> constraint ption
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <50093BBD.6080007 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 7/20/12 6:46 AM, radhika jaswal wrote:
> > Dear all,
> >
> > I did NVT simulations of a number of molecules with
> double bond. But when i analysed the results i realised that
> double bond has been converted to single bond and sp2
> hybridisation has also changed to sp3. I was doing with all
> bonds constraint option. But when i started with all angles
> constraint option it kept on processing on version 3.3.1
> and with many fatal errors on version 4.5.4.
>
> Bonds do not break and form in classical MD, and
> hybridization cannot change.
> If you are observing distortions in the structure, then
> likely your topology is
> ill-suited to address the atoms involved. Correct use
> of improper dihedrals
> should keep sp2 groups planar.
>
> <snip>
>
Dear Sir,
I am using the ffG43a1 force field. Mine is an unusual unusual peptide and got the necessary files from prodrg server.
and also pasting the top file. Please tell where , m making the mistake.
The Force Fields to be included
#include "ffG43a1.itp"
; Include nmab2 topology
#include "nmab2.itp"
; Include water topology
#include "spc.itp"
; Include position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
#ifdef POSRE_WATER
; Position Restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
[ system ]
; Name
DRG in water
[ molecules ]
; Compound #mols
DRG 1
SOL 397
Thanks Sir.
Radhika
> -------------------------------------------------------
> > Program mdrun, VERSION 4.5.4
> > Source code file: domdec.c, line: 6436
> >
> > Fatal error:
> > There is no domain decomposition for 8 nodes that is
> compatible with the given box and a minimum cell size of
> 1.69222 nm
> > Change the number of nodes or mdrun option -rcon or
> your LINCS settings
> > Look in the log file for details on the domain
> decomposition
> > For more information and tips for troubleshooting,
> please check the GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> -------------------------------------------------------
> >
>
> Not all systems can be divided into any arbitrary number of
> DD cells. See here:
>
> http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 20 Jul 2012 09:46:13 -0300
> From: Sebastien Cote <sebastien.cote.4 at umontreal.ca>
> Subject: [gmx-users] CHARMM36 - Smaller Area per lipid for
> POPE - Why?
> To: <gmx-users at gromacs.org>
> Message-ID: <BAY167-W11121360369F5B617C5AB3EBED80 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Dear Gromacs users,
>
> My simulations on a POPE membrane using the CHARMM36
> parameters are giving ''area per lipid'' values well below
> the experimental value (59.75-60.75 Angstroms2). Is their
> someone else experiencing a similar problem? If yes, how did
> you solved it?
>
> I did the following :
>
> I used the CHARMM36 parameters kindly provided by Thomas J.
> Piggot on the Users contribution section on Gromacs
> website.
> My starting configuration was taken from : http://terpconnect.umd.edu/~jbklauda/research/download.html
> It is a POPE membrane of 80 lipids equilibrated in NPT at
> T=310K and P=1atm for 40 ns. It is taken from the article
> Klauda, J. B. et al. 2010 J. Phys. Chem. B, 114, 7830-7843.
>
> At first, I tested normal TIP3P vs. CHARMM TIP3P and saw
> that normal TIP3P gives smaller Area per lipid of about 2-3
> Angstroms. This was also observed by T.J. Piggot (personnal
> communication) and Tieleman (Sapay, N. et al. 2010 J. Comp.
> Chem. 32, 1400-1410). So, I will present only the
> simulations using CHARMM TIP3P. As in Klauda's paper, my
> simulations are at 310K and 1 atm. As them, I used a switch
> cutoff for vdw, and I used normal cutoff for PME. The
> simulations are 20 ns. I can send my .mdp file for more
> details. I varied the switch condition on vdw :
>
> 1- For a switch from 0.8 to 1.2 (as in Klauda's paper), I
> got Area per lipid of about 56.5 Angstroms2; whereas they
> got 59.2 in their paper, matching the experimental value of
> 59.75-60.75.
> 2- For a switch from 1.0 to 1.2, I got Area per lipid of
> about 53.5 Angstroms2, which is smaller than the previous
> cutoff. This is surprising since a previous thread on
> gromacs-users mailing lists said that increasing the lower
> cutoff, increased the Area per lipid or had not impact on
> POPC of DPPC.
> 3- For a switch from 1.1 to 1.2, I got Area per lipid of
> about 55 Angstroms2.
> 4- For a hard cutoff at 1.4, I got Area per lipid of about
> 52 Angstroms2.
>
> I also tried to re-equilibrate the membrane in the NPAT
> ensemble for 10 ns at 310K and 1 atm. Then, when I launched
> the simulation in NPT, I ended up with different results :
>
> 1- Switch from 0.8 to 1.2 gave a smaller area per lipid of
> 54 Angstroms2.
> 2- Switch from 1.0 to 1.2 gave a larger area per lipid of 55
> Angstroms2.
> 4- Hard cutoff at 1.4 gave a similar area per lipid of 52.5
> Angstroms2.
>
> I looked at the POPE paramaters for CHARMM36 in Gromacs, and
> they agree with the published parameters.
>
> Am I doing anything wrong? Is their someone else
> experiencing a similar problem for POPE? If yes, how did you
> solved it?
>
> Should I instead use CHARMM27 parameters in the NPAT
> ensemble? I want to study the interaction between a peptide
> and the POPE membrane. I am troubled that the NPAT ensemble
> might influence my results in a bad way. Also, I can not use
> OPLS AA nor GROMOS for the protein interactions because
> these force fields are not giving the correct structural
> ensemble for my peptide in solution.
>
> I am willing to send more information if you need.
>
> Thanks a lot,
> Sincerely,
>
> Sébastien
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 20 Jul 2012 15:32:10 +0200
> From: francesco oteri <francesco.oteri at gmail.com>
> Subject: [gmx-users] is NOASSEMBLYLOOPS broken?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>
> <CAFQcp-Nip4t9gWZfG6qY2iXMcZCca2DwS8+=rSZ_D4-f9bXzdA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear gromacs users (and eventually developers too),
> I am trying to debug gromacs and on the gromacs website
> http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer's_Guide#local_index
>
> It is stated:
>
> "gromacs can be forced to use non assembly routines to do
> force
> calculations (easier to debug) by defining
> "NOASSEMBLYLOOPS=1" as
> environment variable (e.g. put "export NOASSEMBLYLOOPS=1"
> without the
> quotes in your /etc/profile)"
>
> I tried to use this approach, but it doesn't work since gdb
> goes
> inside the assembly loop.
>
> Moreover, in order to check spelling errors I got each
> getenv call:
>
> grep -R getenv `find -name *.c`
>
>
> ./src/kernel/fflibutil.c: lib =
> getenv("GMXLIB");
> ./src/kernel/runner.c: if ((env =
> getenv("GMX_MAX_THREADS")) != NULL)
> ./src/kernel/runner.c:
> getenv("GMXGHAT"),inputrec, (Flags & MD_REPRODUCIBLE));
> ./src/kernel/readir.c: if (getenv("GALACTIC_DYNAMICS")
> == NULL) {
> ./src/kernel/pdb2gmx.c: bFFRTPTERRNM =
> (getenv("GMX_NO_FFRTP_TER_RENAME") == NULL);
> ./src/kernel/do_gct.c: if ((buf =
> getenv("DISTGCT")) == NULL)
> ./src/kernel/md.c: if
> (getenv("GMX_FORCE_UPDATE"))
> ./src/ngmx/logo.c: if ((newcol=getenv("LOGO"))!=NULL)
> ./src/ngmx/x11.c: fontname=getenv("GMXFONT");
> ./src/ngmx/x11.c: display=getenv("DISPLAY");
> ./src/contrib/do_multiprot.c: if
> ((mptr=getenv("MULTIPROT")) == NULL) {
> ./src/contrib/do_shift.c: if ((dptr=getenv("TOTAL"))
> == NULL)
> ./src/gmxlib/tpxio.c:
> env = getenv("GMX_NOCHARGEGROUPS");
> ./src/gmxlib/checkpoint.c: if
> (getenv(GMX_IGNORE_FSYNC_FAILURE_ENV)==NULL)
> ./src/gmxlib/checkpoint.c:
> if
> (getenv("GMX_ALLOW_CPT_MISMATCH") == NULL)
> ./src/gmxlib/statutil.c: select =
> getenv("GMXTIMEUNIT");
> ./src/gmxlib/statutil.c: select =
> getenv("GMX_VIEW_XVG");
> ./src/gmxlib/statutil.c: envstr =
> getenv("GMXNPRIALL");
> ./src/gmxlib/statutil.c: envstr =
> getenv("GMXNPRI");
> ./src/gmxlib/mtop_util.c: env =
> getenv("GMX_MAXRESRENUM");
> ./src/gmxlib/disre.c: ptr =
> getenv("GMX_DISRE_ENSEMBLE_SIZE");
> ./src/gmxlib/viewit.c: if (getenv("DISPLAY") ==
> NULL) {
> ./src/gmxlib/viewit.c: if ( !
> (cmd=getenv(env)) ) {
> ./src/gmxlib/viewit.c: if (
> getenv("XMGR") )
> ./src/gmxlib/viewit.c: if ( !
> (cmd=getenv(env)) )
> ./src/gmxlib/enxio.c: if
> (getenv("GMX_ENX_NO_FATAL") != NULL)
> ./src/gmxlib/main.c: if
> (getenv(GMX_CHECK_MPI_ENV) == NULL)
> ./src/gmxlib/network.c: if (getenv("GMX_NO_NODECOMM")
> == NULL) {
> ./src/gmxlib/gmx_fatal.c: if
> ((temp=getenv("WHERE")) != NULL)
> ./src/gmxlib/futil.c: env =
> getenv("GMX_MAXBACKUP");
> ./src/gmxlib/futil.c: if
> (bUnbuffered ||
> ((bufsize=getenv("LOG_BUFS")) != NULL)) {
> ./src/gmxlib/futil.c:
> if (!found && (s=getenv("PATH")) != NULL)
> ./src/gmxlib/futil.c: lib=getenv("GMXLIB");
> ./src/gmxlib/copyrite.c: return
> (getenv("GMX_NO_QUOTES") == NULL);
> ./src/gmxlib/vmdio.c: pathenv =
> getenv("VMD_PLUGIN_PATH");
> ./src/gmxlib/txtdump.c: if (getenv("LONGFORMAT") !=
> NULL)
> ./src/gmxlib/sighandler.c: if
> (getenv("GMX_NO_TERM") == NULL)
> ./src/gmxlib/sighandler.c: if
> (getenv("GMX_NO_INT") == NULL)
> ./src/gmxlib/sighandler.c: if
> (getenv("GMX_NO_USR1") == NULL)
> ./src/gmxlib/nonbonded/nonbonded.c:
> if(getenv("GMX_NOOPTIMIZEDKERNELS") != NULL)
> ./src/mdlib/shellfc.c:
> shfc->bPredict =
> (getenv("GMX_NOPREDICT") == NULL);
> ./src/mdlib/shellfc.c: shfc->bForceInit =
> (getenv("GMX_FORCEINIT") != NULL);
> ./src/mdlib/qm_orca.c: buf = getenv("BASENAME");
> ./src/mdlib/qm_orca.c: buf = getenv("ORCA_PATH");
> ./src/mdlib/ns.c: fr->ns.bCGlist =
> (getenv("GMX_NBLISTCG") != 0);
> ./src/mdlib/ns.c: char
> *ptr=getenv("GMX_DUMP_NL");
> ./src/mdlib/tpi.c: ptr =
> getenv("GMX_TPIC_MASSES");
> ./src/mdlib/tpi.c: dump_pdb = getenv("GMX_TPI_DUMP");
> ./src/mdlib/forcerec.c: if
> (getenv("GMX_NO_SOLV_OPT"))
> ./src/mdlib/forcerec.c:
> getenv("GMX_NO_ALLVSALL") == NULL
> ./src/mdlib/forcerec.c: env =
> getenv("GMX_SCSIGMA_MIN");
> ./src/mdlib/forcerec.c: if
> (getenv("GMX_NB_GENERIC") != NULL)
> ./src/mdlib/forcerec.c:
> fr->UseOptimizedKernels =
> (getenv("GMX_NOOPTIMIZEDKERNELS") == NULL);
> ./src/mdlib/forcerec.c: if
> (getenv("GMX_FORCE_TABLES"))
> ./src/mdlib/qm_gaussian.c: buf =
> getenv("NCPUS");
> ./src/mdlib/qm_gaussian.c: buf =
> getenv("MEM");
> ./src/mdlib/qm_gaussian.c: buf =
> getenv("ACC");
> ./src/mdlib/qm_gaussian.c: buf =
> getenv("CPMCSCF");
> ./src/mdlib/qm_gaussian.c: buf =
> getenv("SASTEP");
> ./src/mdlib/qm_gaussian.c: buf =
> getenv("GAUSS_DIR");
> ./src/mdlib/qm_gaussian.c: buf =
> getenv("GAUSS_EXE");
> ./src/mdlib/qm_gaussian.c: buf =
> getenv("DEVEL_DIR");
> ./src/mdlib/qm_gaussian.c: * environment
> using getenv().
> ./src/mdlib/qm_gaussian.c: buf =
> getenv("STATE");
> ./src/mdlib/constr.c: char
> *env=getenv("GMX_SUPPRESS_DUMP");
> ./src/mdlib/constr.c: env =
> getenv("GMX_MAXCONSTRWARN");
> ./src/mdlib/gmx_wallcycle.c: if (PAR(cr)
> &&
> getenv("GMX_CYCLE_BARRIER") != NULL)
> ./src/mdlib/gmx_wallcycle.c: if
> (getenv("GMX_CYCLE_ALL") != NULL)
> ./src/mdlib/nsgrid.c: ptr =
> getenv("GMX_NSCELL_NCG");
> ./src/mdlib/mdebin.c:
> md->bConstrVir =
> (getenv("GMX_CONSTRAINTVIR") != NULL);
> ./src/mdlib/mdebin.c:
> md->bEner[i] = (EI_DYNAMICS(ir->eI)
> && getenv("GMX_VIRIAL_TEMPERATURE"));
> ./src/mdlib/mdebin.c: bNoseHoover =
> (getenv("GMX_NOSEHOOVER_CHAINS") != NULL); /* whether to
> print
> Nose-Hoover chains */
> ./src/mdlib/mdebin.c: bNoseHoover
> =
> (getenv("GMX_NOSEHOOVER_CHAINS") != NULL);
> ./src/mdlib/pull.c: if
> (getenv("GMX_NO_PULLVIR") != NULL)
> ./src/mdlib/partdec.c: cap_env =
> getenv("GMX_CAPACITY");
> ./src/mdlib/domdec.c: CartReorder =
> (getenv("GMX_NO_CART_REORDER") == NULL);
> ./src/mdlib/domdec.c: val = getenv(env_var);
> ./src/mdlib/domdec.c: if
> (getenv("GMX_DD_ORDER_ZYX") != NULL)
> ./src/mdlib/domdec.c:
> getenv("GMX_PMEONEDD") == NULL)
> ./src/tools/gmx_tune_pme.c: if (
> (cp = getenv("MPIRUN")) != NULL)
> ./src/tools/gmx_tune_pme.c: if ( (cp =
> getenv("MDRUN" )) != NULL )
> ./src/tools/gmx_eneconv.c: if ((getenv("VERBOSE")) !=
> NULL)
> ./src/tools/do_dssp.c: if ((dptr=getenv("DSSP")) ==
> NULL)
> ./src/tools/gmx_cluster.c: if (getenv("TESTMC")) {
> ./src/tools/gmx_dipoles.c: if ((ptr =
> getenv("GKRWIDTH")) != NULL) {
> ./src/tools/gmx_membed.c: if
> (getenv("GMX_FORCE_UPDATE"))
> ./src/tools/gmx_membed.c:
> getenv("GMXGHAT"),inputrec, (Flags & MD_REPRODUCIBLE));
> ./src/tools/gmx_energy.c: if ((getenv("VERBOSE")) !=
> NULL)
> ./src/tools/gmx_energy.c: if ((getenv("VERBOSE")) !=
> NULL)
> ./src/tools/gmx_wham.c:
> if(!(Path=getenv("GMX_PATH_GZIP")))
>
> Interestingly, NOASSEMBLYLOOPS it is never checkd but the
> variable
> GMX_NOOPTIMIZEDKERNELS seems to have the same meaning.
> Is this an undocumented changement?
>
> What about the documentation of the internal environment
> variable in
> gromacs discussed in
> http://lists.gromacs.org/pipermail/gmx-developers/2012-March/005714.html
> ?
>
>
> Francesco
>
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
> before posting!
>
> End of gmx-users Digest, Vol 99, Issue 79
> *****************************************
>
More information about the gromacs.org_gmx-users
mailing list