Re: [gmx-users] output energies by group
Hi Yuguang, you don't have to wait your mdrun job to finish to check out your energies,trajectories. Just use "g_energy" and you'll get the energies up to the last frame wrote on .edr file. Diego Enry. On 8/4/06, Mu Yuguang (Dr) <[EMAIL PROTECTED]> wrote: Dear all, >> How to output energies of different groups during the MD simulation? >with g_energy, if you have used energy groups in the simulation... No, I mean output the group energies in the flying ( using cut-off, during the simulation, not after the simulation), I think I have to modify the source code. > > Best regards > Yuguang > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] output energies by group
Dear all, >> How to output energies of different groups during the MD simulation? >with g_energy, if you have used energy groups in the simulation... No, I mean output the group energies in the flying ( using cut-off, during the simulation, not after the simulation), I think I have to modify the source code. > > Best regards > Yuguang > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2
Dear Erik, I had the same problem as Arthur Roberts. So I downloaded your new version of gmx_system_xdr.h and gmx_system_xdr.c from http://bugzilla.gromacs.org/show_bug.cgi?id=55 Before I recompile gromacs, I checked the difference between your new version and the old one. The result is as follows: diff gmx_system_xdr.c gmx_system_xdr-n.c 2c2 < * $Id: gmx_system_xdr.c,v 1.5.4.1 2006/03/09 08:12:16 lindahl Exp $ --- > * $Id: gmx_system_xdr.c,v 1.5 2004/01/23 17:23:13 lindahl Exp $ diff gmx_system_xdr.h gmx_system_xdr-n.h 2c2 < * $Id: gmx_system_xdr.h,v 1.3.4.1 2006/03/09 08:12:09 lindahl Exp $ --- > * $Id: gmx_system_xdr.h,v 1.3 2003/11/17 21:50:40 spoel Exp $ Both differences are in documentation. I am confused how your modification can solve the problem. I had the same problem and posted in the mailing list before ( http://www.gromacs.org/pipermail/gmx-users/2006-June/022493.html ) I also found Jason O'Young had asked the similar question at http://www.gromacs.org/pipermail/gmx-users/2006-May/021605.html I think this problem sounds common, could you please investigate what's wrong? Thank you very much for your help! By the way, I can continue the simulation by tpbconv, but hangs soon without any error message. The "top" command shows the programs is running, but no more output data. All the best! Dongsheng On Mon, 2006-07-31 at 08:36 +0200, Erik Lindahl wrote: > Hi, > > It _might_ be solved by the fix attachment at > > http://bugzilla.gromacs.org/show_bug.cgi?id=55 > > (also in CVS) > > Cheers, > > Erik > > On Jul 31, 2006, at 8:11 AM, Arthur Roberts wrote: > > > Hi, all, > > > > I am trying to run Gromacs on a P655+ with Aix 5.2. > > Initially, mdrun appears to work, but always hangs. > > Eventually, I get timed out from the supercomputer > > with no data to show for it. Below is a link > > detailing the problem: > > > > http://cetus.mchem.washington.edu/pub/supercomputer/Mdrun-hangs- > > without-showing-steps.html > > > > I appreciate your input. Your previous suggestions > > have been very helpful. > > > > Best wishes, > > Art > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb2gmx and ignh
Hello all, I am confused about what the -ignh option of pdb2gmx actually does. I have read the mailing list, the manual and many tutorials and short of browsing the source cannot find a definite answer. The man page claims that pdb2gmx will add hydrogens, however after using the ignh option to ignore inappropriately named hydrogens in the input pdb (1xq8.pdb) there are many missing hydrogens (nearly a thousand - as far as I can tell) in the output files. Running any calculation with that many missing hydrogens seems very non-physical. It seems that pdb2gmx doesn't like the naming conventions or number of hydrogens in the pdb file. Can someone please explain what -ignh actually does and what the proper method of converting a pdb file from RCSB for use with GROMACS should be? I have tried building the protein from scratch with pymol but pdb2gmx doesn't like pymol generated pdb files either. begin:vcard fn:Frisco Rose n:Rose;Frisco org:Center for High Performance Simulation;Physics, North Carolina State University adr:851 Main Campus Dr.;;Partners III Room 120E;Raleigh;NC;27695;US email;internet:[EMAIL PROTECTED] title:Graduate Research Assistant tel;work:(919) 515-7228 tel;fax:(919) 755-0500 tel;home:(919) 832-2538 tel;cell:(919) 345-3329 x-mozilla-html:FALSE url:http://chips.ncsu.edu/~froze version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem with ambconv
Thanks, yes, that would be interesting as I plan on obtaining AMBER. Does it work with any version ? Diane -Original Message- From: [EMAIL PROTECTED] on behalf of David Mobley Sent: Fri 8/4/2006 3:00 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] problem with ambconv Diane, We have an in-house script called amb2gmx written in collaboration with the Pande group that works for this purpose, although it requires an installation of AMBER. Let me know if you would like it. Thanks, David On 8/4/06, Diane Fournier <[EMAIL PROTECTED]> wrote: > > > > Hi > > I'm presently trying to use the ambconv program to convert amber topologies > generated with antechamber v. 1.26 and tleap to gromacs format for use with > the amber force field port. > > The problem is, I can't get the program to work. For example : > > $ ambconv -v -at spl2.atop -rst spl2.rst -gt spl2.itp -gro spl2.gro -pdb > spl2.pdb > AMBCONV v1.0 > AMBER .top : spl2.atop > AMBER .rst : spl2.rst > GROMACS .top : spl2.itp > GROMACS .gro : spl2.gro > PDB .pdb : spl2.pdb > Segmentation fault > > This is using the old file format generated with tleap when setting > oldprmtopformat to on. The same happens with the new file formats (.prmtop > and .inpcrd). > I have tried modifying the ambconv.c file and recompiling as suggested in > the mailing list (Wed Jun 16 18:41:55 CEST 2004), but got the same result. > > Does someone has a version of ambconv which works with antechamber 1.26, or > should I use an older version of antechamber and leap ? > > Diane > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with ambconv
Diane, We have an in-house script called amb2gmx written in collaboration with the Pande group that works for this purpose, although it requires an installation of AMBER. Let me know if you would like it. Thanks, David On 8/4/06, Diane Fournier <[EMAIL PROTECTED]> wrote: Hi I'm presently trying to use the ambconv program to convert amber topologies generated with antechamber v. 1.26 and tleap to gromacs format for use with the amber force field port. The problem is, I can't get the program to work. For example : $ ambconv -v -at spl2.atop -rst spl2.rst -gt spl2.itp -gro spl2.gro -pdb spl2.pdb AMBCONV v1.0 AMBER .top : spl2.atop AMBER .rst : spl2.rst GROMACS .top : spl2.itp GROMACS .gro : spl2.gro PDB .pdb : spl2.pdb Segmentation fault This is using the old file format generated with tleap when setting oldprmtopformat to on. The same happens with the new file formats (.prmtop and .inpcrd). I have tried modifying the ambconv.c file and recompiling as suggested in the mailing list (Wed Jun 16 18:41:55 CEST 2004), but got the same result. Does someone has a version of ambconv which works with antechamber 1.26, or should I use an older version of antechamber and leap ? Diane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with ambconv
Title: problem with ambconv Hi I'm presently trying to use the ambconv program to convert amber topologies generated with antechamber v. 1.26 and tleap to gromacs format for use with the amber force field port. The problem is, I can't get the program to work. For example : $ ambconv -v -at spl2.atop -rst spl2.rst -gt spl2.itp -gro spl2.gro -pdb spl2.pdb AMBCONV v1.0 AMBER .top : spl2.atop AMBER .rst : spl2.rst GROMACS .top : spl2.itp GROMACS .gro : spl2.gro PDB .pdb : spl2.pdb Segmentation fault This is using the old file format generated with tleap when setting oldprmtopformat to on. The same happens with the new file formats (.prmtop and .inpcrd). I have tried modifying the ambconv.c file and recompiling as suggested in the mailing list (Wed Jun 16 18:41:55 CEST 2004), but got the same result. Does someone has a version of ambconv which works with antechamber 1.26, or should I use an older version of antechamber and leap ? Diane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] output energies by group
Mu Yuguang (Dr) wrote: Dear all, How to output energies of different groups during the MD simulation? with g_energy, if you have used energy groups in the simulation... Best regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv problem
hi, similar happened to me, when i used the -b and -e flags of trjconv. to me it seemed that if you do not hit exactly the time frame as written in the trr file, trjconv will not output anything. when i used the -dump flag it worked, because then frames near the specified time are dumped. hope that helps. marc On Friday 04 August 2006 16:05, Bjoern Windshuegel wrote: > Hi everybody, > > I am trying to extract some frames from my md simulation using trjconv. For > some frames this works fine but for others of the same simulation I get the > following error message (for frame after 5590 picoseconds): > > Skipping frame500 time 5250.000 > > Setting output precision to 0.001 (nm) > > WARNING no output, trajectory ended at 5590 > > > The trajectory has a length of 10 ns. I could successfully extract frames > for 4310 and 8950 but not 3110, 5590 and 7020 picoseconds. Any idea what > could be the problem? > > > Best regards, > > Björn ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] output energies by group
Dear all, How to output energies of different groups during the MD simulation? Best regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv problem
Bjoern Windshuegel wrote: Hi everybody, I am trying to extract some frames from my md simulation using trjconv. For some frames this works fine but for others of the same simulation I get the following error message (for frame after 5590 picoseconds): Skipping frame500 time 5250.000 Setting output precision to 0.001 (nm) WARNING no output, trajectory ended at 5590 The trajectory has a length of 10 ns. I could successfully extract frames for 4310 and 8950 but not 3110, 5590 and 7020 picoseconds. Any idea what could be the problem? Best regards, Björn It might be a rouding problem, so if you want to extract the single frame at time 5590, you might want to try trjconv -b 5589.9 -e 5590.1 -o frame.pdb ... If it still doesn't work: In gromacs 3.3 there was a bug that caused trjconv not to find frames. As far as I know the bug was fixed in Version 3.3.1. cheers, jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trjconv problem
Hi everybody, I am trying to extract some frames from my md simulation using trjconv. For some frames this works fine but for others of the same simulation I get the following error message (for frame after 5590 picoseconds): Skipping frame500 time 5250.000 Setting output precision to 0.001 (nm) WARNING no output, trajectory ended at 5590 The trajectory has a length of 10 ns. I could successfully extract frames for 4310 and 8950 but not 3110, 5590 and 7020 picoseconds. Any idea what could be the problem? Best regards, Björn -- Bjoern Windshuegel Department of Pharmaceutical Chemistry University of Kuopio Harjulantie 1 70211 Kuopio, FINLAND Phone: (+358) 17 162463 Fax: (+358) 17 162456 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
