[gmx-users] valgrind warnigs with git mdrun
Hi, I am implementing some addition stuff to mdrun, but my mdrun (in particle decomposition) stops with lincs warings after running fine for 10 to 50 ps or so. The same system with the git master does not crash (with -pd), which, of course, does not mean there is no memory leak as well. So I was running my system with the git master mdrun within valgrind --leak-check=yes, and got the following warnings (see below), which eventually stop in a fatal error: Program mdrun_debug, VERSION 4.0.99_development_20090927 Source code file: mshift.c, line: 647 Fatal error: No GREY nodes found while nG=4 I am now wondering if that is a valgrind problem or if mdrun has a problem that shows up as crashes in my altered version of mdrun. Thanks for any hints, Jochen ps: I have compiled mdrun on a linux with an intel compiler via: export LDFLAGS=-L/opt/fftw/3.2/icc11/lib export CPPFLAGS=-I/opt/fftw/3.2/icc11/include source /opt/intel/ictce/3.2.1.015/ictvars.sh export CC=icc export I_MPI_CC=icc export LD=icc export CFLAGS=-g -O0 make distclean ./configure --prefix=/home/jhub/src/git/gmx-master/build.debug --without-x --enable-mpi --program-suffix=_debug --disable-shared --without-xml During compilation, I get the following warnings. Don't know if they are a problem though: ../../../../include/gmx_sse2_single.h(251): warning #167: argument of type __m128i is incompatible with parameter of type __m128 xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base)); ^ ../../../../include/gmx_sse2_single.h(251): warning #167: argument of type __m128i is incompatible with parameter of type __m128 xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base)); ../../include/gmx_sse2_single.h(251): warning #167: argument of type __m128i is incompatible with parameter of type __m1 28 xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base)); ^ resall.c(488): warning #167: argument of type const char * is incompatible with parameter of type char * n=neq_str(key,rtp[i].resname); ^ grompp.c(306): warning #592: variable mbs is used before its value is set mbs; ^ valgrind output: * Getting Loaded... Reading file test.with-normal-grompp.tpr, VERSION 4.0.99_development_20090927 (single precision) ^[[BLoaded with Money Getting Loaded... Reading file test.with-normal-grompp.tpr, VERSION 4.0.99_development_20090927 (single precision) Loaded with Money ==6218== Invalid read of size 4 ==6218==at 0x53A866: mk_grey (mshift.c:528) ==6218==by 0x53B010: mk_mshift (mshift.c:657) ==6218==by 0x4CA095: low_do_pbc_mtop (sim_util.c:1295) ==6218==by 0x4CA168: do_pbc_first_mtop (sim_util.c:1314) ==6218==by 0x412AAD: mdrunner (runner.c:545) ==6218==by 0x411972: mdrunner_threads (runner.c:196) ==6218==by 0x41DAC0: main (mdrun.c:515) ==6218== Address 0x5add7f8 is 8 bytes inside a block of size 457,016 free'd ==6218==at 0x4A05F1D: realloc (vg_replace_malloc.c:476) ==6218==by 0x5547C5: save_realloc (smalloc.c:196) ==6218==by 0x53996A: compact_graph (mshift.c:260) ==6218==by 0x539F1D: mk_graph_ilist (mshift.c:364) ==6218==by 0x4CA03B: low_do_pbc_mtop (sim_util.c:1291) ==6218==by 0x4CA168: do_pbc_first_mtop (sim_util.c:1314) ==6218==by 0x412AAD: mdrunner (runner.c:545) ==6218==by 0x411972: mdrunner_threads (runner.c:196) ==6218==by 0x41DAC0: main (mdrun.c:515) ==6218== Getting Loaded... Reading file test.with-normal-grompp.tpr, VERSION 4.0.99_development_20090927 (single precision) ^[[BLoaded with Money ==6025== Invalid read of size 4 ==6025==at 0x53A866: mk_grey (mshift.c:528) ==6025==by 0x53B010: mk_mshift (mshift.c:657) ==6025==by 0x4CA095: low_do_pbc_mtop (sim_util.c:1295) ==6025==by 0x4CA168: do_pbc_first_mtop (sim_util.c:1314) ==6025==by 0x412AAD: mdrunner (runner.c:545) ==6025==by 0x411972: mdrunner_threads (runner.c:196) ==6025==by 0x41DAC0: main (mdrun.c:515) ==6025== Address 0x5add7f8 is 8 bytes inside a block of size 457,016 free'd ==6025==at 0x4A05F1D: realloc (vg_replace_malloc.c:476) ==6025==by 0x5547C5: save_realloc (smalloc.c:196) ==6025==by 0x53996A: compact_graph (mshift.c:260) ==6025==by 0x539F1D: mk_graph_ilist (mshift.c:364) ==6025==by 0x4CA03B: low_do_pbc_mtop (sim_util.c:1291) ==6025==by 0x4CA168: do_pbc_first_mtop (sim_util.c:1314) ==6025==by 0x412AAD: mdrunner (runner.c:545) ==6025==by 0x411972: mdrunner_threads (runner.c:196) ==6025==by 0x41DAC0: main (mdrun.c:515) ==6025== ==6025== Invalid read of size 4 ==6025==at 0x4DDD2C: init_vcm (vcm.c:78) ==6025==by 0x4CA70E: init_md (sim_util.c:1457) ==6025==by 0x41617A: do_md (md.c:969) ==6025==by 0x4133D1: mdrunner (runner.c:669) ==6025==by 0x411972: mdrunner_threads (runner.c:196) ==6025==by 0x41DAC0: main (mdrun.c:515) ==6025== Address 0x57a80d4 is 0 bytes after a block of size 4 alloc'd ==6025==
[gmx-users] density problems when switching from md to sd integrator
Dear users, I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K, compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds). After equilibration and NPT simulation, the system reaches the proper density reported for the model (791g/L). When I switch to a stochastic integrator (with inverse friction coeff. tau_t=0.2 ps) the density rapidly falls to about 765g/L, the potential energy increases, while temperature and pressure fluctuate much more around their specified values. I intend to use this box of cyclohexane for solvation free energy calculations. Can anyone explain what is going on? Thanks in advance Aymeric attachment: anaome.vcf-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] valgrind warnigs with git mdrun
Hi, First of all, Gromacs is full of memory leaks, which by itself it not so nice, but this is not a problem (unless we are eating up all the memory). I guess you meant to say illegal memory access iso memory leaks. The current valgrind warnings in the graph code are due to a bug in valgrind. I have thoroughly checked this code, especially because of the valgrind warnings. The sse2 warnings should be checked. Berk Date: Thu, 28 Jan 2010 10:28:59 +0100 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] valgrind warnigs with git mdrun Hi, I am implementing some addition stuff to mdrun, but my mdrun (in particle decomposition) stops with lincs warings after running fine for 10 to 50 ps or so. The same system with the git master does not crash (with -pd), which, of course, does not mean there is no memory leak as well. So I was running my system with the git master mdrun within valgrind --leak-check=yes, and got the following warnings (see below), which eventually stop in a fatal error: Program mdrun_debug, VERSION 4.0.99_development_20090927 Source code file: mshift.c, line: 647 Fatal error: No GREY nodes found while nG=4 I am now wondering if that is a valgrind problem or if mdrun has a problem that shows up as crashes in my altered version of mdrun. Thanks for any hints, Jochen ps: I have compiled mdrun on a linux with an intel compiler via: export LDFLAGS=-L/opt/fftw/3.2/icc11/lib export CPPFLAGS=-I/opt/fftw/3.2/icc11/include source /opt/intel/ictce/3.2.1.015/ictvars.sh export CC=icc export I_MPI_CC=icc export LD=icc export CFLAGS=-g -O0 make distclean ./configure --prefix=/home/jhub/src/git/gmx-master/build.debug --without-x --enable-mpi --program-suffix=_debug --disable-shared --without-xml During compilation, I get the following warnings. Don't know if they are a problem though: ../../../../include/gmx_sse2_single.h(251): warning #167: argument of type __m128i is incompatible with parameter of type __m128 xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base)); ^ ../../../../include/gmx_sse2_single.h(251): warning #167: argument of type __m128i is incompatible with parameter of type __m128 xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base)); ../../include/gmx_sse2_single.h(251): warning #167: argument of type __m128i is incompatible with parameter of type __m1 28 xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base)); ^ resall.c(488): warning #167: argument of type const char * is incompatible with parameter of type char * n=neq_str(key,rtp[i].resname); ^ grompp.c(306): warning #592: variable mbs is used before its value is set mbs; ^ _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp gives no molecules were defined in the system
Hi, I have a problem with Gromacs. I want to do MD simulations with my proteïn in a DPPC-membrane. Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I just used a bigger membrane (256 lipids instead of 128). I managed to correctly embed the proteïn in the bilayer, I solvated it with genbox and then I want to add ions. But when I use grompp to get a .tpr file for genion, Gromacs fives the following error: Program grompp, VERSION 4.0.7 Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320 Fatal error: No molecules were defined in the system I did update my topology in the [ molecules ] section and checked it twice to see if it fits with the .gro file. It is correct, so I don't know what the problem is. Before the solvation there was no problem with grompp, so it must have something to do with the solvation? I hope someone can help me. Thanks, Marysa van den Berg _ Alles over Windows http://www.windows.nl/About.aspx-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] workshop for Gromacs
Dear Gromacs Developers, I'm intested in a workshop for Gromacs. Is there a workshop planned in 2010 ? Kind Regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] workshop for Gromacs
Hi, please see: http://tfy.tkk.fi/soft/levi2010/ Rasoul On Thu, Jan 28, 2010 at 12:42 PM, oguz gurbulak gurbulako...@yahoo.comwrote: Dear Gromacs Developers, I'm intested in a workshop for Gromacs. Is there a workshop planned in 2010 ? Kind Regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp gives no molecules were defined in the system
Hi Marysa, The error is about the definition of mulecules, which suggests that there are no [ moleculetype ] directives. Did you #include the proper .itp file(s) with the necessary moleculetype definitions? If not, you'll have to provide more information, probably posting the topology file itself. Cheers, Tsjerk On Thu, Jan 28, 2010 at 12:27 PM, Marysa van den Berg mvdberg1...@hotmail.com wrote: Hi, I have a problem with Gromacs. I want to do MD simulations with my proteïn in a DPPC-membrane. Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I just used a bigger membrane (256 lipids instead of 128). I managed to correctly embed the proteïn in the bilayer, I solvated it with genbox and then I want to add ions. But when I use grompp to get a .tpr file for genion, Gromacs fives the following error: Program grompp, VERSION 4.0.7 Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320 Fatal error: No molecules were defined in the system I did update my topology in the [ molecules ] section and checked it twice to see if it fits with the .gro file. It is correct, so I don't know what the problem is. Before the solvation there was no problem with grompp, so it must have something to do with the solvation? I hope someone can help me. Thanks, Marysa van den Berg Minder SPAM in de verbeterde Windows Live Hotmail -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp gives no molecules were defined in the system
Do you have the right number of atoms indicated on the second line of the .gro file? What is in your [molecules] directive in your topology? -Justin Marysa van den Berg wrote: Hi, I have a problem with Gromacs. I want to do MD simulations with my proteïn in a DPPC-membrane. Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I just used a bigger membrane (256 lipids instead of 128). I managed to correctly embed the proteïn in the bilayer, I solvated it with genbox and then I want to add ions. But when I use grompp to get a .tpr file for genion, Gromacs fives the following error: /Program grompp, VERSION 4.0.7 Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320/ /Fatal error: No molecules were defined in the system / I did update my topology in the [ molecules ] section and checked it twice to see if it fits with the .gro file. It is correct, so I don't know what the problem is. Before the solvation there was no problem with grompp, so it must have something to do with the solvation? I hope someone can help me. Thanks, Marysa van den Berg Minder SPAM in de verbeterde Windows Live Hotmail http://mail.live.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] HI
I have to recreate .gro file from .trr file by using trjconv which i have deleated previously for disk space reasons , im using following commond for that trjconv -f full.trr -s full.tpr -o fullout.gro . so my question is will this commond give me the same gro file that it was previously or it may variate or any changes that u suggest in the given commond. my second question is regarding g_rms, i created the .xvg for g_rms , the grph shows it has continous run for molecule with some peaks in between why is it so as im doing analysis for the first time i dont know what does this indicates . is it because the molecule is jumping across the box ? so that more rmsd at that place ,i think by using -nojump i can do this ? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] HI
Please use a descriptive subject line. Simply using Hi will often not attract the attention of someone who can help you, and other times will get trapped in a spam filter, depending on the settings of the server or email client. pavan payghan wrote: I have to recreate .gro file from .trr file by using trjconv which i have deleated previously for disk space reasons , im using following commond for that trjconv -f full.trr -s full.tpr -o fullout.gro . so my question is will this commond give me the same gro file that it was previously or it may variate or any changes that u suggest in the given commond. No, this will give you the entire trajectory in .gro format, which is likely a very large file. Use gmxcheck to see for yourself. my second question is regarding g_rms, i created the .xvg for g_rms , the grph shows it has continous run for molecule with some peaks in between why is it so as im doing analysis for the first time i dont know what does this indicates . is it because the molecule is jumping across the box ? so that more rmsd at that place ,i think by using -nojump i can do this ? That depends on what you define as a peak. Small spikes may or may not be reasonable, depending on what your structure is doing. If these spikes are very large, they could correspond to your molecule crossing PBC, in which case you would have to use trjconv. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mpi_run issue
Hi,
I tried to run the command
mdrun -deffnm em
on cluster,
blow is the script, but I worried that it might be some place wrong, seems no
files came out after several hours running
Is anyone please help me to modify it, and how can know the process of its
running in the cluster.
Thanks and best regards,
Elsa
#!/bin/bash
#
## Specify the job name
#PBS -N emMDrunSecondOne
## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
PBS_O_WORKDIR=${HOME}/Jobs/1A7W/tryScript
[ -d ${PBS_O_WORKDIR}] || exit 1
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS
## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em
exit 0
winmail.dat--
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[gmx-users] hblife
Hi, would you please elaborate the first column in the hblife.xvg file? hblife.xyg is the output of the following command: g_hbond -life hblife.xvg this column don't show the real time in simulated system.what are these times? thanks in advance, Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] hblife
afsaneh maleki wrote: Hi, would you please elaborate the first column in the hblife.xvg file? hblife.xyg is the output of the following command: g_hbond -life hblife.xvg this column don't show the real time in simulated system.what are these times? Check the headers in the .xvg file; the output of the analysis tools generally writes axis labels and data set legends. If it still doesn't make sense, post a snippet of your file. -Justin thanks in advance, Afsaneh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] density problems when switching from md to sd integrator
Dear Aymeric: 1. Can we please see the entire .mdp files for both simulations? I suggest that you use a tau_t=1.0 (0.2 is probably over-damped). 2. Although any value of tau_t should still produce the correct equilibria, your diffusion rates and your overall sampling may be slower with sd tau_t=0.2 than they are with md. 3. Can you reproduce this effect with a box of water? -- original message -- I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K, compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds). After equilibration and NPT simulation, the system reaches the proper density reported for the model (791g/L). When I switch to a stochastic integrator (with inverse friction coeff. tau_t=0.2 ps) the density rapidly falls to about 765g/L, the potential energy increases, while temperature and pressure fluctuate much more around their specified values. I intend to use this box of cyclohexane for solvation free energy calculations. Can anyone explain what is going on? Thanks in advance Aymeric -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] hblife
thanks dear justin' it is right that the output of the analysis tools generally writes axis labels and data set legends. in hblife.xyg file is written that x axis label Time (ps) and the last time is written 14300.001 whereas my simulated time is 4 ps not 143000.00 ps i send you this file Best wishes, Afsaneh On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Hi, would you please elaborate the first column in the hblife.xvg file? hblife.xyg is the output of the following command: g_hbond -life hblife.xvg this column don't show the real time in simulated system.what are these times? Check the headers in the .xvg file; the output of the analysis tools generally writes axis labels and data set legends. If it still doesn't make sense, post a snippet of your file. -Justin thanks in advance, Afsaneh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- hblife.xvg Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mpi_run issue
- Original Message -
From: #ZHAO LINA# zhao0...@ntu.edu.sg
Date: Friday, January 29, 2010 1:11
Subject: [gmx-users] mpi_run issue
To: gmx-users@gromacs.org
Hi,
I tried to run the command
mdrun -deffnm em
on cluster,
blow is the script, but I worried that it might be some place
wrong, seems no files came out after several hours running
Is anyone please help me to modify it, and how can know the
process of its running in the cluster.
We can't know the best procedure for your cluster because we haven't read its
documentation or talked to its admins... (hint, hint)
Thanks and best regards,
Elsa
#!/bin/bash
#
## Specify the job name
#PBS -N emMDrunSecondOne
## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
PBS_O_WORKDIR=${HOME}/Jobs/1A7W/tryScript
[ -d ${PBS_O_WORKDIR}] || exit 1
This looks wrong. PBS usually has flags that let you specify running the job in
directory from which submission occured - use them.
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS
If PBS is defining $PBS_NODEFILE to point to some file it creates, then that
file won't be local to the directory you've arbitrarily changed to, so NCPUS
won't get defined suitably, so mpirun won't work.
I'd suggest you start again from some example script that is known to work on
your cluster and modify only the mpirun line.
Mark
## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em
exit 0
--
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Re: [gmx-users] hblife
afsaneh maleki skrev: thanks dear justin' it is right that the output of the analysis tools generally writes axis labels and data set legends. in hblife.xyg file is written that x axis label Time (ps) and the last time is written 14300.001 whereas my simulated time is 4 ps not 143000.00 ps i send you this file I don't remember the details about the calculation of lifetimes, but I believe it's an estimate of how the half lifes of hydrogen bonds. You can also get this quantity, along with the kinetic constants and energies for hb breaking and frormation, using -ac. If I remember correctly, -ac uses a more reliable method. Erik Best wishes, Afsaneh On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: afsaneh maleki wrote: Hi, would you please elaborate the first column in the hblife.xvg file? hblife.xyg is the output of the following command: g_hbond -life hblife.xvg this column don't show the real time in simulated system.what are these times? Check the headers in the .xvg file; the output of the analysis tools generally writes axis labels and data set legends. If it still doesn't make sense, post a snippet of your file. -Justin thanks in advance, Afsaneh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] hblife
- Original Message - From: afsaneh maleki maleki.afsa...@gmail.com Date: Friday, January 29, 2010 1:56 Subject: Re: [gmx-users] hblife To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org thanks dear justin' it is right that the output of the analysis tools generally writes axis labels and data set legends. in hblife.xyg file is written that x axis label Time (ps) and the last time is written 14300.001 whereas my simulated time is 4 ps not 143000.00 ps Axis labels are different from legend labels. Please cite the full command line, not an abbreviated one. The .xvg shows the full line. Other options can have effects on the output, though it is not clear if/why that might be true here. Try a simple g_hbond -life calculation and see if it differs. Mark i send you this file Best wishes, Afsaneh On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Hi, would you please elaborate the first column in the hblife.xvg file? hblife.xyg is the output of the following command: g_hbond -life hblife.xvg this column don't show the real time in simulated system.what are these times? Check the headers in the .xvg file; the output of the analysis tools generally writes axis labels and data set legends. If it still doesn't make sense, post a snippet of your file. -Justin thanks in advance, Afsaneh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] hblife
- Original Message - From: Mark Abraham mark.abra...@anu.edu.au Date: Friday, January 29, 2010 2:16 Subject: Re: [gmx-users] hblife To: Discussion list for GROMACS users gmx-users@gromacs.org - Original Message - From: afsaneh maleki maleki.afsa...@gmail.com Date: Friday, January 29, 2010 1:56 Subject: Re: [gmx-users] hblife To: jalem...@vt.edu, Discussion list for GROMACS users gmx- us...@gromacs.org thanks dear justin' it is right that the output of the analysis tools generally writes axis labels and data set legends. in hblife.xyg file is written that x axis label Time (ps) and the last time is written 14300.001 whereas my simulated time is 4 ps not 143000.00 ps Axis labels are different from legend labels. Please cite the full command line, not an abbreviated one. The .xvg shows the full line. Other options can have effects on the output, though it is not clear if/why that might be true here. Try a simple g_hbond -life calculation and see if it differs. It won't. Now that my brain is turned on, you're just getting what you asked for, which is a frequency plot of H-bond lifetimes. Evidently you have none which persist longer than 14.3ns. Mark Mark i send you this file Best wishes, Afsaneh On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Hi, would you please elaborate the first column in the hblife.xvg file? hblife.xyg is the output of the following command: g_hbond -life hblife.xvg this column don't show the real time in simulated system.what are these times? Check the headers in the .xvg file; the output of the analysis tools generally writes axis labels and data set legends. If it still doesn't make sense, post a snippet of your file. -Justin thanks in advance, Afsaneh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: gmx-users Digest, Vol 69, Issue 145
Hi,
Here is the example file I based on to modify,
mpi.sh
#!/bin/bash
#
## Specify the job name
#PBS -N jobname
## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
## pre-processing script
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS
## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE ./myprog
My working directory is ${HOME}/Jobs/1A7W/tryScript. By the way, I do not know
the NODEFILE mean.
Thanks and best regards,
Elsa
--
Hi,
I tried to run the command
mdrun -deffnm em
on cluster,
blow is the script, but I worried that it might be some place
wrong, seems no files came out after several hours running
Is anyone please help me to modify it, and how can know the
process of its running in the cluster.
We can't know the best procedure for your cluster because we haven't read its
documentation or talked to its admins... (hint, hint)
Thanks and best regards,
Elsa
#!/bin/bash
#
## Specify the job name
#PBS -N emMDrunSecondOne
## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
PBS_O_WORKDIR=${HOME}/Jobs/1A7W/tryScript
[ -d ${PBS_O_WORKDIR}] || exit 1
This looks wrong. PBS usually has flags that let you specify running the job in
directory from which submission occured - use them.
cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS
If PBS is defining $PBS_NODEFILE to point to some file it creates, then that
file won't be local to the directory you've arbitrarily changed to, so NCPUS
won't get defined suitably, so mpirun won't work.
I'd suggest you start again from some example script that is known to work on
your cluster and modify only the mpirun line.
Mark
## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em
exit 0
--
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Message: 2
Date: Thu, 28 Jan 2010 16:03:50 +0100
From: Erik Marklund er...@xray.bmc.uu.se
Subject: Re: [gmx-users] hblife
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4b61a756.7060...@xray.bmc.uu.se
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
afsaneh maleki skrev:
thanks dear justin'
it is right that the output of the analysis tools generally writes
axis labels and data set legends. in hblife.xyg file is written that
x axis label Time (ps) and the last time is written 14300.001
whereas my simulated time is 4 ps not 143000.00 ps
i send you this file
I don't remember the details about the calculation of lifetimes, but I
believe it's an estimate of how the half lifes of hydrogen bonds. You
can also get this quantity, along with the kinetic constants and
energies for hb breaking and frormation, using -ac. If I remember
correctly, -ac uses a more reliable method.
Erik
Best wishes,
Afsaneh
On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
afsaneh maleki wrote:
Hi,
would you please elaborate the first column in the hblife.xvg
file?
hblife.xyg is the output of the following command:
g_hbond -life hblife.xvg
this column don't show the real time in simulated system.what
are these times?
Check the headers in the .xvg file; the output of the analysis
tools generally writes axis labels and data set legends. If it
still doesn't make sense, post a snippet of your file.
-Justin
thanks in advance,
Afsaneh
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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Please search the archive at http://www.gromacs.org/search before
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[gmx-users] Rotational PMF using angle_restraints_z and virtual definition
Hello, I am attempting to construct the free energy profile for rotation of a short peptide hairpin. For this purpose, I am using [ angle_restraints_z ]. I will focus this post on the simplified test system that I have been using to characterize the problem that I am experiencing: single peptide in vacuo using the sd integrator. The free energy profile for rotation here should be flat (After entropic debiasing). However, I do not find a flat PMF. I find that the PMF (generated by WHAM) has local maxima at every center of restraint. This indicates over-sampling at distances away from each center of restraint and if I input a lower force constant to WHAM (400 kJ/mol in place of the 500 kJ/mol that I used for sampling), I can indeed get a flat PMF. So it seems to me that there is some problem with either i) the sampling or with ii) the post-sampling analysis of sampled positions. I have ruled out some obvious possibilities for option ii: a) The stored angles accurately reproduce the sampled angles as checked by comparison to g_energy; b) The modified version of WHAM that I am using (angle_restraints_z is non-harmonic) successfully produces a flat PMF with fake data generated based on a MC generation program that I wrote. Further, the local-maxima-at-centers-of-restraint problem is not alleviated by increasing the window overlap. Importantly, I'm using a highly unusual virtual atom architecture to get at this angle to the z-axis because I was unable to define a COM group for this purpose. I do end up defining the angle between two COMs, but I do it via i) generation of a number of [ virtual_sites2 ] : [ virtual_sites2 ] ;sites from funct a1 28852 239 1 0.5 Where I eventually utilize virtual atom 288 as one atom in the definition of angle_restraints_z. Note that atoms 52 and 239 are not virtual. [ angle_restraints_z ] 138 288 1 0 500 1 I have created a test system in which I take a water molecule and place a virtual atom between the two hydrogens and do similar [ angle_restraints_z ] on the angle between the oxygen and the new virtual atom -- here I do not see the effect. I have also tested not using the virtual site in my peptide simulation, using instead: [ angle_restraints_z ] 138 239 1 0 500 1 and in this case I also do not see the effect. And ideas about what could be going on or test systems that I might try? My best guess is that by putting the restraint on a virtual_sites2 atom, I am not doing exactly what I think I am doing, but I have no idea what the difference might be. Thank you, Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_order in GMX4.05
Hello everyone, I use the g_order to get the order parameter of the tails( C1A, C2A, C3A, C4A) of DPPC. The are 100 molecules of DPPC 1. I use the make_ndx -f dppc.trr -n index to produce the index file. a C1A a C2A a C3A a C4A del 0-3 Q_1: Is the method right to produce the index file? Then there only four groups orderly named C1A, C2A, C3A, C4A in the index file. 2. I use the g_order -n index -s npt.tpr ... to get the order parameter. However, there are lots of errors . WARNING: distance between atoms 29777 and 29779 0.3 nm (0.897513). Index file might be corrupt. WARNING: distance between atoms 29789 and 29791 0.3 nm (0.709495). Index file might be corrupt. WARNING: distance between atoms 29801 and 29803 0.3 nm (0.692954). Index file might be corrupt. WARNING: distance between atoms 29813 and 29815 0.3 nm (0.784918). Index file might be corrupt. WARNING: distance between atoms 29825 and 29827 0.3 nm (0.839048). Index file might be corrupt. WARNING: distance between atoms 29837 and 29839 0.3 nm (0.851105). Index file might be corrupt. WARNING: distance between atoms 29849 and 29851 0.3 nm (0.790752). Index file might be corrupt. WARNING: distance between atoms 29861 and 29863 0.3 nm (0.836583). Index file might be corrupt. WARNING: distance between atoms 29873 and 29875 0.3 nm (0.854105). Index file might be corrupt. WARNING: distance between atoms 29885 and 29887 0.3 nm (0.847901). Index file might be corrupt. WARNING: distance between atoms 29897 and 29899 0.3 nm (0.758556). Index file might be corrupt. ... Why? 3. Result Last frame 4 time 240.000 Read trajectory. Printing parameters to file Atom 1 Tensor: x=-0.267416 , y=-0.245994, z=0.51341 Atom 2 Tensor: x=-0.207203 , y=-0.171233, z=0.378436 Back Off! I just backed up order.xvg to ./#order.xvg.1# Back Off! I just backed up deuter.xvg to ./#deuter.xvg.1# gcq#51: The Stingrays Must Be Fat This Year (Red Hot Chili Peppers) [tia...@localhost dppcden5]$ cat order.xvg # This file was created Sun Apr 23 10:10:35 2006 # by the following command: # g_order -f traj.trr -n index.ndx -s npt.tpr -o -e 240 # # g_order is part of G R O M A C S: # # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon # @title Order tensor diagonal elements @xaxis label Atom @yaxis label S @TYPE xy 1 -0.267416 -0.2459940.51341 2 -0.207203 -0.171233 0.378436 [tia...@localhost dppcden5]$ -- wende -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_order in GMX4.05
lammps lammps wrote: Hello everyone, I use the g_order to get the order parameter of the tails( C1A, C2A, C3A, C4A) of DPPC. The are 100 molecules of DPPC 1. I use the make_ndx -f dppc.trr -n index to produce the index file. a C1A a C2A a C3A a C4A del 0-3 Q_1: Is the method right to produce the index file? There is a how-to on the g_order page: http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order Your procedure seems like it might be right, but what are atoms C1A, C2A, etc? This isn't the numbering I'm used to. What are groups 0-3? Then there only four groups orderly named C1A, C2A, C3A, C4A in the index file. 2. I use the g_order -n index -s npt.tpr ... to get the order parameter. However, there are lots of errors Don't use ... when posting a command. Provide the whole command. . WARNING: distance between atoms 29777 and 29779 0.3 nm (0.897513). Index file might be corrupt. WARNING: distance between atoms 29789 and 29791 0.3 nm (0.709495). Index file might be corrupt. WARNING: distance between atoms 29801 and 29803 0.3 nm (0.692954). Index file might be corrupt. WARNING: distance between atoms 29813 and 29815 0.3 nm (0.784918). Index file might be corrupt. WARNING: distance between atoms 29825 and 29827 0.3 nm (0.839048). Index file might be corrupt. WARNING: distance between atoms 29837 and 29839 0.3 nm (0.851105). Index file might be corrupt. WARNING: distance between atoms 29849 and 29851 0.3 nm (0.790752). Index file might be corrupt. WARNING: distance between atoms 29861 and 29863 0.3 nm (0.836583). Index file might be corrupt. WARNING: distance between atoms 29873 and 29875 0.3 nm (0.854105). Index file might be corrupt. WARNING: distance between atoms 29885 and 29887 0.3 nm (0.847901). Index file might be corrupt. WARNING: distance between atoms 29897 and 29899 0.3 nm (0.758556). Index file might be corrupt. ... Why? These messages seem to indicate that you have non-sequential carbon atoms. Cross-check the atom names you've used to create the index file with the actual coordinates. -Justin 3. Result Last frame 4 time 240.000 Read trajectory. Printing parameters to file Atom 1 Tensor: x=-0.267416 , y=-0.245994, z=0.51341 Atom 2 Tensor: x=-0.207203 , y=-0.171233, z=0.378436 Back Off! I just backed up order.xvg to ./#order.xvg.1# Back Off! I just backed up deuter.xvg to ./#deuter.xvg.1# gcq#51: The Stingrays Must Be Fat This Year (Red Hot Chili Peppers) [tia...@localhost dppcden5]$ cat order.xvg # This file was created Sun Apr 23 10:10:35 2006 # by the following command: # g_order -f traj.trr -n index.ndx -s npt.tpr -o -e 240 # # g_order is part of G R O M A C S: # # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon # @title Order tensor diagonal elements @xaxis label Atom @yaxis label S @TYPE xy 1 -0.267416 -0.2459940.51341 2 -0.207203 -0.171233 0.378436 [tia...@localhost dppcden5]$ -- wende -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] including a custom itp file in topology
Hi, I was trying to figure out if there is a short-cut for what I'm doing. I have complexes that I'm trying to prep using pdb2gmx. The ligand does not have a standard residue name. The way I know this can work is seperating out the ligand and protein into seperate files and preping the ligand using acpypi and the protein using pdb2gmx. Then incorporating them into a single pdb complex and including a reference to the ligand.itp (generated by acpypi) into a complex topology file. Is there any shortcut to doing this? any way to reference the ligand's itp file when running pdb2gmx? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] amidated C-terminus in the charmm ff port for gromacs
Hi everybody I am currently testing the CHARMM port for GROMACS pre4.1. I have downloaded the c32b1_release_1.1.zip file http://www.dbb.su.se/User:Bjelkmar/Ffcharmm (11:59, 23 Oct 2009). My protein protein have an acetylated N-terminus and amidated C-terminus. According to the CHARMM force field, these groups are considered as two residus named ACE and CT2, respectively. In the ffcharmm27.rtp, only the statement ACE, NMA are presents, where is the CT2 group in the file? Thank you in advance for your help. Stephane winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] grompp gives no molecules were defined in the system
Hi, The number of atoms in the second line of my .gro file are correct, I checked that. This is what my topology file says in the beginning: [ moleculetype ] ; Name nrexcl Protein 3 No changes here after the solvation. At the end after the [ atoms ] directive: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong po sition restraints for InflateGro #ifdef STRONG_POSRES #include strong_posre.itp endif ; Include DPPC chain topology #include dppc.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcy fcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein1 DPPC 242 SOL 48333 The only thing in the topology that changed after the solvation, was adding the watermolecules in the [ molecules ] section (SOL 48333) What could be the problem? Thanks, Marysa _ 25GB gratis online harde schijf http://skydrive.live.com-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp gives no molecules were defined in the system
Marysa van den Berg wrote: Hi, The number of atoms in the second line of my .gro file are correct, I checked that. This is what my topology file says in the beginning: [ moleculetype ] ; Name nrexcl Protein 3 No changes here after the solvation. At the end after the [ atoms ] directive: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong po sition restraints for InflateGro #ifdef STRONG_POSRES #include strong_posre.itp endif Here's the problem. To end the #ifdef statement, you need #endif, not endif. Since you haven't closed the #ifdef, nothing is being found after this point in the topology (assuming you're not specifying define = -DSTRONG_POSRES in the .mdp file, which you only want at certain times). -Justin ; Include DPPC chain topology #include dppc.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcy fcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein1 DPPC 242 SOL 48333 The only thing in the topology that changed after the solvation, was adding the watermolecules in the [ molecules ] section (SOL 48333) What could be the problem? Thanks, Marysa Ontdek nu Windows phone. De smartphone van dit moment http://www.microsoft.com/windowsmobile/nl-nl/default.mspx -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:mpi_run issue
/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- 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/search before posting! End of gmx-users Digest, Vol 69, Issue 145 ** -- next part -- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 8300 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20100128/9f005516/attachment.bin -- -- 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/search before posting! End of gmx-users Digest, Vol 69, Issue 146 ** winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re:mpi_run issue
don't show the real time in simulated system.what are these times? Check the headers in the .xvg file; the output of the analysis tools generally writes axis labels and data set legends. If it still doesn't make sense, post a snippet of your file. -Justin thanks in advance, Afsaneh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- 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/search before posting! End of gmx-users Digest, Vol 69, Issue 145 ** -- next part -- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 8300 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx- users/attachments/20100128/9f005516/attachment.bin -- -- 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/search before posting! End of gmx-users Digest, Vol 69, Issue 146 ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] including a custom itp file in topology
- Original Message - From: Jack Shultz j...@drugdiscoveryathome.com Date: Friday, January 29, 2010 4:15 Subject: [gmx-users] including a custom itp file in topology To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Alan alanwil...@gmail.com, Andrey Voronkov a...@drugdiscoveryathome.com Hi, I was trying to figure out if there is a short-cut for what I'm doing. I have complexes that I'm trying to prep using pdb2gmx. The ligand does not have a standard residue name. The way I know this can work is seperating out the ligand and protein into seperate files and preping the ligand using acpypi and the protein using pdb2gmx. Then incorporating them into a single pdb complex and including a reference to the ligand.itp (generated by acpypi) into a complex topology file. Is there any shortcut to doing this? any way to reference the ligand's itp file when running pdb2gmx? The procedure looks good, but there's no way to get pdb2gmx to do this step for you. It will be straightforward to use sed or perl to add the #include and the [molecules] changes into the .top produced by pdb2gmx - that's what these tools are for! Even head -n -2 topol.top new.top echo '#include ligand.itp' new.top tail -n 2 topol.top footer new.top echo 'ligand 1' new.top will do the job if the last two lines of topol.top are of the form [molecules] Protein 1 This kind of UNIX-tool scripted problem-solving using head, tail, cut, paste, grep, sed, uniq, sort, echo, perl, cat and others often requires some consultation of the man pages and awareness that the tool exists... but most problems you want to solve have been solved before and the tool is out there already... Google away! Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] warning and PME
Hi, while perform simulation, I perceive nether warning , I recourse page 87147manual (PME part ),but I can 't understand that how apply change in the .mdp file according to said direction in the nether warning . please guide me, how remove error. consist warning : Can not exclude the lattice Coulomb energy between energy groups Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 42x42x125, 0.120 0.119 0.119 NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 2 Mb of data writing run input file... Thaks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] warning and PME
On 29/01/10 14:54, neo lotus wrote: Hi, while perform simulation, I perceive nether warning , I recourse page 87147manual (PME part ),but I can 't understand that how apply change in the .mdp file according to said direction in the nether warning . please guide me, how remove error. consist warning : Can not exclude the lattice Coulomb energy between energy groups By its very nature, you can't exclude Ewald-style long-range Coulomb interactions between different groups. Perhaps some more background reading is in order. Then, reconsider your choice of the combination of PME and energy exclusions. Mark Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 42x42x125, 0.120 0.119 0.119 NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 2 Mb of data writing run input file... Thaks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Vacuum FF in Gromacs-4.0.5
Hi, I wanted to inquire about the vacuum FF distributed officially with GROMACS-4.0.5. I wish to carry out a vacuum MD of ~300 aa protein FF.dat file mentions of G43b1 as officially distributed vacuum FF. But there are no FF related files-.rtp,.hdb etc present. Is that the case that GROMACS-4 is improperly installed at my end or do I have to get these FF files from some external source ? Regards, Nikhil The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Vacuum FF in Gromacs-4.0.5
Hi, I removed this force field on purpose. The name is already very confusing. It is not a vacuum force field at all. It is an implicit solvent force field, but a quite bad one. It only scales down the charges on groups with net charge. If you really want to simulate a protein in vacuum do NOT use this force field. If you really, really want to use this force field, download an old Gromacs distribution and copy the parameter files. Berk Date: Fri, 29 Jan 2010 12:23:02 +0530 From: pdnik...@yahoo.co.in To: gmx-users@gromacs.org Subject: [gmx-users] Vacuum FF in Gromacs-4.0.5 Hi, I wanted to inquire about the vacuum FF distributed officially with GROMACS-4.0.5. I wish to carry out a vacuum MD of ~300 aa protein FF.dat file mentions of G43b1 as officially distributed vacuum FF. But there are no FF related files-.rtp,.hdb etc present. Is that the case that GROMACS-4 is improperly installed at my end or do I have to get these FF files from some external source ? Regards, Nikhil The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Vacuum FF in Gromacs-4.0.5
On 1/29/10 8:29 AM, Berk Hess wrote: Hi, I removed this force field on purpose. The name is already very confusing. It is not a vacuum force field at all. It is an implicit solvent force field, but a quite bad one. It only scales down the charges on groups with net charge. If you really want to simulate a protein in vacuum do NOT use this force field. If you really, really want to use this force field, download an old Gromacs distribution and copy the parameter files. It depends on what you want to do. If you want to simulate what happens to a protein under vacuum conditions you could use a normal force field, but you have to consider which sidechains are charged. See e.g.: Biochemistry 46 pp. 933-945 (2007) http://pubs.acs.org/cgi-bin/download.pl?bi061182y/B6CC or Phys. Chem. Chem. Phys. 11 pp. 8069-8078 (2009) http://dx.doi.org/10.1039/b903846a Berk Date: Fri, 29 Jan 2010 12:23:02 +0530 From: pdnik...@yahoo.co.in To: gmx-users@gromacs.org Subject: [gmx-users] Vacuum FF in Gromacs-4.0.5 Hi, I wanted to inquire about the vacuum FF distributed officially with GROMACS-4.0.5. I wish to carry out a vacuum MD of ~300 aa protein FF.dat file mentions of G43b1 as officially distributed vacuum FF. But there are no FF related files-.rtp,.hdb etc present. Is that the case that GROMACS-4 is improperly installed at my end or do I have to get these FF files from some external source ? Regards, Nikhil The INTERNET now has a personality. YOURS! See your Yahoo! Homepage http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/. Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
