--- On Fri, 20/7/12, gmx-users-requ...@gromacs.org <gmx-users-requ...@gromacs.org> wrote:
> From: gmx-users-requ...@gromacs.org <gmx-users-requ...@gromacs.org> > Subject: gmx-users Digest, Vol 99, Issue 79 > To: gmx-users@gromacs.org > Date: Friday, 20 July, 2012, 7:09 PM > Send gmx-users mailing list > submissions to > gmx-users@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-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@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 <jaswalradh...@yahoo.co.in> > Subject: [gmx-users] Please help with all-angles constraint > ption > To: gmx-users@gromacs.org > Message-ID: > <1342781163.38035.yahoomailclas...@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 <jalem...@vt.edu> > Subject: Re: [gmx-users] Please help with all-angles > constraint ption > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <50093bbd.6080...@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.cot...@umontreal.ca> > Subject: [gmx-users] CHARMM36 - Smaller Area per lipid for > POPE - Why? > To: <gmx-users@gromacs.org> > Message-ID: <bay167-w11121360369f5b617c5ab3ebe...@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.ot...@gmail.com> > Subject: [gmx-users] is NOASSEMBLYLOOPS broken? > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > > <CAFQcp-Nip4t9gWZfG6qY2iXMcZCca2DwS8+=rsz_d4-f9bx...@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@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 > ***************************************** > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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