[gmx-users] Random option - genion
Dear users, can anyone tell me if the random option (genion program) was set to always stay in the yes state? I'm trying to set -random no (just a test), but it didn't work at all. Thanks in advance, Mauricio -- gmx-users mailing listgmx-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! 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/Support/Mailing_Lists
Re: [gmx-users] Random option - genion
Thank you very much, Justin. Mauricio 2012/3/1 Justin A. Lemkul jalem...@vt.edu Maurício Menegatti Rigo wrote: Dear users, can anyone tell me if the random option (genion program) was set to always stay in the yes state? I'm trying to set -random no (just a test), but it didn't work at all. The default is yes. To invoke the opposite (which is true for all Gromacs options), the syntax is genion -norandom. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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! 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/Support/Mailing_Lists
[gmx-users] Memory allocation - xpm2ps
Hi, I found the following error when I tried to run xpm2ps. *** glibc detected *** xpm2ps: realloc(): invalid pointer: 0x00dd0541 *** === Backtrace: = /lib/libc.so.6[0x7f20a53b0dd6] /lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1] xpm2ps(save_realloc+0x5e)[0x43741e] xpm2ps[0x42cf24] xpm2ps(read_xpm_entry+0x2fe)[0x42d88e] xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2] xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000] /lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd] xpm2ps[0x412949] === Memory map: 0040-005e3000 r-xp fc:03 7799252 /usr/local/gromacs/bin/xpm2ps 007e2000-007e3000 r-xp 001e2000 fc:03 7799252 /usr/local/gromacs/bin/xpm2ps 007e3000-007e9000 rwxp 001e3000 fc:03 7799252 /usr/local/gromacs/bin/xpm2ps 007e9000-007ea000 rwxp 00:00 0 00dce000-00def000 rwxp 00:00 0 [heap] 7f20a5124000-7f20a513a000 r-xp fc:03 17400029 /lib/libgcc_s.so.1 7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029 /lib/libgcc_s.so.1 7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029 /lib/libgcc_s.so.1 7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029 /lib/libgcc_s.so.1 7f20a533b000-7f20a54a1000 r-xp fc:03 17400032 /lib/libc-2.10.1.so 7f20a54a1000-7f20a56a ---p 00166000 fc:03 17400032 /lib/libc-2.10.1.so 7f20a56a-7f20a56a4000 r-xp 00165000 fc:03 17400032 /lib/libc-2.10.1.so 7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032 /lib/libc-2.10.1.so 7f20a56a5000-7f20a56aa000 rwxp 00:00 0 7f20a56aa000-7f20a56c1000 r-xp fc:03 17400305 /lib/libpthread-2.10.1.so 7f20a56c1000-7f20a58c ---p 00017000 fc:03 17400305 /lib/libpthread-2.10.1.so 7f20a58c-7f20a58c1000 r-xp 00016000 fc:03 17400305 /lib/libpthread-2.10.1.so 7f20a58c1000-7f20a58c2000 rwxp 00017000 fc:03 17400305 /lib/libpthread-2.10.1.so 7f20a58c2000-7f20a58c6000 rwxp 00:00 0 7f20a58c6000-7f20a58c8000 r-xp fc:03 17401201 /lib/libutil-2.10.1.so 7f20a58c8000-7f20a5ac7000 ---p 2000 fc:03 17401201 /lib/libutil-2.10.1.so 7f20a5ac7000-7f20a5ac8000 r-xp 1000 fc:03 17401201 /lib/libutil-2.10.1.so 7f20a5ac8000-7f20a5ac9000 rwxp 2000 fc:03 17401201 /lib/libutil-2.10.1.so 7f20a5ac9000-7f20a5acb000 r-xp fc:03 17400035 /lib/libdl-2.10.1.so 7f20a5acb000-7f20a5ccb000 ---p 2000 fc:03 17400035 /lib/libdl-2.10.1.so 7f20a5ccb000-7f20a5ccc000 r-xp 2000 fc:03 17400035 /lib/libdl-2.10.1.so 7f20a5ccc000-7f20a5ccd000 rwxp 3000 fc:03 17400035 /lib/libdl-2.10.1.so 7f20a5ccd000-7f20a5d1b000 r-xp fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0 7f20a5d1b000-7f20a5f1b000 ---p 0004e000 fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0 7f20a5f1b000-7f20a5f1c000 r-xp 0004e000 fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0 7f20a5f1c000-7f20a5f1e000 rwxp 0004f000 fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0 7f20a5f1e000-7f20a5f41000 rwxp 00:00 0 7f20a5f41000-7f20a5f89000 r-xp fc:03 7921099 /usr/local/lib/libopen-rte.so.0.0.0 Aborted I note that someone already had the same problem. Could someone tell me if this was fixed? I'm using the gromacs version 4.5.1, in an i7 processor. Thanks in advance, -- Maurício M. Rigo -- gmx-users mailing listgmx-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! 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/Support/Mailing_Lists
Re: [gmx-users] Memory allocation - xpm2ps
Hi, Thank you for your answer. Unfortunately, I can't fix my problem. I dont know if I'm doing this right, but first I type the line *git clone git://git.gromacs.org/gromacs.git* in the command line. After all the outputs, I tried to run xpm2ps again, but occured the same error. 2010/10/15 Justin A. Lemkul jalem...@vt.edu Maurício Menegatti Rigo wrote: Hi, I found the following error when I tried to run xpm2ps. *** glibc detected *** xpm2ps: realloc(): invalid pointer: 0x00dd0541 *** === Backtrace: = /lib/libc.so.6[0x7f20a53b0dd6] /lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1] xpm2ps(save_realloc+0x5e)[0x43741e] xpm2ps[0x42cf24] xpm2ps(read_xpm_entry+0x2fe)[0x42d88e] xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2] xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000] /lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd] xpm2ps[0x412949] === Memory map: 0040-005e3000 r-xp fc:03 7799252 /usr/local/gromacs/bin/xpm2ps 007e2000-007e3000 r-xp 001e2000 fc:03 7799252 /usr/local/gromacs/bin/xpm2ps 007e3000-007e9000 rwxp 001e3000 fc:03 7799252 /usr/local/gromacs/bin/xpm2ps 007e9000-007ea000 rwxp 00:00 0 00dce000-00def000 rwxp 00:00 0 [heap] 7f20a5124000-7f20a513a000 r-xp fc:03 17400029 /lib/libgcc_s.so.1 7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029 /lib/libgcc_s.so.1 7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029 /lib/libgcc_s.so.1 7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029 /lib/libgcc_s.so.1 7f20a533b000-7f20a54a1000 r-xp fc:03 17400032 /lib/libc-2.10.1.so http://libc-2.10.1.so 7f20a54a1000-7f20a56a ---p 00166000 fc:03 17400032 /lib/libc-2.10.1.so http://libc-2.10.1.so 7f20a56a-7f20a56a4000 r-xp 00165000 fc:03 17400032 /lib/libc-2.10.1.so http://libc-2.10.1.so 7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032 /lib/libc-2.10.1.so http://libc-2.10.1.so 7f20a56a5000-7f20a56aa000 rwxp 00:00 0 7f20a56aa000-7f20a56c1000 r-xp fc:03 17400305 /lib/libpthread-2.10.1.so http://libpthread-2.10.1.so 7f20a56c1000-7f20a58c ---p 00017000 fc:03 17400305 /lib/libpthread-2.10.1.so http://libpthread-2.10.1.so 7f20a58c-7f20a58c1000 r-xp 00016000 fc:03 17400305 /lib/libpthread-2.10.1.so http://libpthread-2.10.1.so 7f20a58c1000-7f20a58c2000 rwxp 00017000 fc:03 17400305 /lib/libpthread-2.10.1.so http://libpthread-2.10.1.so 7f20a58c2000-7f20a58c6000 rwxp 00:00 0 7f20a58c6000-7f20a58c8000 r-xp fc:03 17401201 /lib/libutil-2.10.1.so http://libutil-2.10.1.so 7f20a58c8000-7f20a5ac7000 ---p 2000 fc:03 17401201 /lib/libutil-2.10.1.so http://libutil-2.10.1.so 7f20a5ac7000-7f20a5ac8000 r-xp 1000 fc:03 17401201 /lib/libutil-2.10.1.so http://libutil-2.10.1.so 7f20a5ac8000-7f20a5ac9000 rwxp 2000 fc:03 17401201 /lib/libutil-2.10.1.so http://libutil-2.10.1.so 7f20a5ac9000-7f20a5acb000 r-xp fc:03 17400035 /lib/libdl-2.10.1.so http://libdl-2.10.1.so 7f20a5acb000-7f20a5ccb000 ---p 2000 fc:03 17400035 /lib/libdl-2.10.1.so http://libdl-2.10.1.so 7f20a5ccb000-7f20a5ccc000 r-xp 2000 fc:03 17400035 /lib/libdl-2.10.1.so http://libdl-2.10.1.so 7f20a5ccc000-7f20a5ccd000 rwxp 3000 fc:03 17400035 /lib/libdl-2.10.1.so http://libdl-2.10.1.so 7f20a5ccd000-7f20a5d1b000 r-xp fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0 7f20a5d1b000-7f20a5f1b000 ---p 0004e000 fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0 7f20a5f1b000-7f20a5f1c000 r-xp 0004e000 fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0 7f20a5f1c000-7f20a5f1e000 rwxp 0004f000 fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0 7f20a5f1e000-7f20a5f41000 rwxp 00:00 0 7f20a5f41000-7f20a5f89000 r-xp fc:03 7921099 /usr/local/lib/libopen-rte.so.0.0.0 Aborted I note that someone already had the same problem. Could someone tell me if this was fixed? There have been several fixes to xpm2ps that are available in the development code. Try the latest git version to see if you still have the same problem. -Justin I'm using the gromacs version 4.5.1, in an i7 processor. Thanks in advance, -- Maurício M. Rigo -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Maurício Menegatti
Re: [gmx-users] Memory allocation - xpm2ps
Hi, I copy the file gmx_xpm2ps from the repository to my gromacs folder /usl/local/gromacs/src/tools (i.e. I substitute the old file by the new one). After that, I run xpm2ps and the problem persisted. Any ideas? PS: I run the same job in another i7, but with gromacs version 4.0.7 installed, and everything occured well. 2010/10/15 Justin A. Lemkul jalem...@vt.edu Maurício Menegatti Rigo wrote: Hi, Thank you for your answer. Unfortunately, I can't fix my problem. I dont know if I'm doing this right, but first I type the line /git clone git://git.gromacs.org/gromacs.git http://git.gromacs.org/gromacs.git/ in the command line. After all the outputs, I tried to run xpm2ps again, but occured the same error. Simply downloading the source code won't fix the problem. You have to install (and then use) the resulting binaries. -Justin 2010/10/15 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Maurício Menegatti Rigo wrote: Hi, I found the following error when I tried to run xpm2ps. *** glibc detected *** xpm2ps: realloc(): invalid pointer: 0x00dd0541 *** === Backtrace: = /lib/libc.so.6[0x7f20a53b0dd6] /lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1] xpm2ps(save_realloc+0x5e)[0x43741e] xpm2ps[0x42cf24] xpm2ps(read_xpm_entry+0x2fe)[0x42d88e] xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2] xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000] /lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd] xpm2ps[0x412949] === Memory map: 0040-005e3000 r-xp fc:03 7799252 /usr/local/gromacs/bin/xpm2ps 007e2000-007e3000 r-xp 001e2000 fc:03 7799252 /usr/local/gromacs/bin/xpm2ps 007e3000-007e9000 rwxp 001e3000 fc:03 7799252 /usr/local/gromacs/bin/xpm2ps 007e9000-007ea000 rwxp 00:00 0 00dce000-00def000 rwxp 00:00 0 [heap] 7f20a5124000-7f20a513a000 r-xp fc:03 17400029 /lib/libgcc_s.so.1 7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029 /lib/libgcc_s.so.1 7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029 /lib/libgcc_s.so.1 7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029 /lib/libgcc_s.so.1 7f20a533b000-7f20a54a1000 r-xp fc:03 17400032 /lib/libc-2.10.1.so http://libc-2.10.1.so http://libc-2.10.1.so 7f20a54a1000-7f20a56a ---p 00166000 fc:03 17400032 /lib/libc-2.10.1.so http://libc-2.10.1.so http://libc-2.10.1.so 7f20a56a-7f20a56a4000 r-xp 00165000 fc:03 17400032 /lib/libc-2.10.1.so http://libc-2.10.1.so http://libc-2.10.1.so 7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032 /lib/libc-2.10.1.so http://libc-2.10.1.so http://libc-2.10.1.so 7f20a56a5000-7f20a56aa000 rwxp 00:00 0 7f20a56aa000-7f20a56c1000 r-xp fc:03 17400305 /lib/libpthread-2.10.1.so http://libpthread-2.10.1.so http://libpthread-2.10.1.so 7f20a56c1000-7f20a58c ---p 00017000 fc:03 17400305 /lib/libpthread-2.10.1.so http://libpthread-2.10.1.so http://libpthread-2.10.1.so 7f20a58c-7f20a58c1000 r-xp 00016000 fc:03 17400305 /lib/libpthread-2.10.1.so http://libpthread-2.10.1.so http://libpthread-2.10.1.so 7f20a58c1000-7f20a58c2000 rwxp 00017000 fc:03 17400305 /lib/libpthread-2.10.1.so http://libpthread-2.10.1.so http://libpthread-2.10.1.so 7f20a58c2000-7f20a58c6000 rwxp 00:00 0 7f20a58c6000-7f20a58c8000 r-xp fc:03 17401201 /lib/libutil-2.10.1.so http://libutil-2.10.1.so http://libutil-2.10.1.so 7f20a58c8000-7f20a5ac7000 ---p 2000 fc:03 17401201 /lib/libutil-2.10.1.so http://libutil-2.10.1.so http://libutil-2.10.1.so 7f20a5ac7000-7f20a5ac8000 r-xp 1000 fc:03 17401201 /lib/libutil-2.10.1.so http://libutil-2.10.1.so http://libutil-2.10.1.so 7f20a5ac8000-7f20a5ac9000 rwxp 2000 fc:03 17401201 /lib/libutil-2.10.1.so http://libutil-2.10.1.so http://libutil-2.10.1.so 7f20a5ac9000-7f20a5acb000 r-xp fc:03 17400035 /lib/libdl-2.10.1.so http://libdl-2.10.1.so http://libdl-2.10.1.so 7f20a5acb000-7f20a5ccb000 ---p 2000 fc:03 17400035 /lib/libdl-2.10.1.so http://libdl-2.10.1.so http://libdl-2.10.1.so 7f20a5ccb000-7f20a5ccc000 r-xp 2000 fc:03 17400035 /lib/libdl-2.10.1.so http://libdl-2.10.1.so http://libdl-2.10.1.so 7f20a5ccc000-7f20a5ccd000 rwxp 3000 fc:03 17400035 /lib/libdl-2.10.1.so http://libdl
[gmx-users] Visualization of trajectories in PyMol
Hi, I'm performing a 10 ns molecular dynamics of a homodimer, using GROMACS. I have no problems during and after the simulation, since I have already analyzed the log files and performed the checking. I was able to see, without any problems, the whole concatenated trajectory file with VMD software. However, when I tried to visualize with PyMol, occurs some problems in the last frames, like wrong bonds and dismantlement of my dimer. I'm already use the parameters *-pbc mol* and *-pbc nojump* with trjconv. Any idea? Thanks in advance, Mauricio -- 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] Visualization of my trajectories in PyMol
Hi, I'm performing a 10 ns molecular dynamics of a homodimer, using GROMACS. I have no problems during and after the simulation, since I have already analyzed the log files and performed the checking. I was able to see, without any problems, the whole concatenated trajectory file with VMD software. However, when I tried to visualize with PyMol, occurs some problems in the last frames, like wrong bonds and dismantlement of my dimer. I'm already use the parameters *-pbc mol* and *-pbc nojump* with trjconv. Any idea? Thanks in advance, Mauricio -- 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_gyrate doubt
Hi, we are working with a protein-ligand system (MHC + peptide). We have computed radius of gyration using the following command line: g_gyrate -f File1.xtc -s File2.tpr -n index.ndx -o GYRATE * File1: refer to concatenated trajectories of our *protein* plus *ligand *during 8ns simulation. We choose the *ligand* group to compute the radius of gyration. My questions are: 1) Which center of mass GROMACS will set: the center of mass of the ligand or of the protein? 2) If the center of mass is the protein, all the atoms of the ligand are used for the radius og gyration calculation? Thanks in advance -- Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul -- 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] h_bond error
Hi, I'm trying to compute H bonds in a protein-ligand system. I got the following error: Program g_hbond, VERSION 4.0.7 Source code file: gmx_hbond.c, line: 565 Fatal error: Error in func_type Position Rest. I use the line *g_hbond -f file.xtc -s file.tpr -n index.ndx -g HBOND_log -num HBOND* *file.xtc = THis is my file with concatenate trajectories.* I didnt find anywhere about this error. Someone know how to fix it? Thanks! -- Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul -- 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] h_bond error
Thanks J. My mistake. -- 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] link gromacs i7
We are using an i7 920 processor to run Gromacs-4.0.7 with openmpi-1.4.1. The simulations run well using 4 threads (using mpirun -np 4 mdrun...) but the performance is worse when we use 6 or 8 threads. Looking for some way to improve our performance we found out this forum and then started to try use threads without openmpi. We compiled gromacs again and used the command line as described here (mdrun -nt 8...), but the following error appears: -- Program mdrun, VERSION 4.0.7 Source code file: mdrun.c, line: 410 Fatal error: GROMACS compiled without threads support - can only use one thread -- But in gromacs-4.0.7 threads are not supposed to be ON by default? -- 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] trn file
HI, I'm extensivally searching at manual, internet, gmx-list but i cant find the solution for this error. I tried to concatenate several .trr files with the following line: trjcat -f File1.trr File2.trr File3.trr File4.trr File5.trr File6.trr File7.trr File8.trr -o FINAL File1 to File4 have no problems. HOwever, from File5 the program present the following error: *Continue writing frames from File5.trr t=30 ps, frame=76 Reading frame 70 time 58.000- frame150 time 59.600 ps --- Program trjcat, VERSION 4.0.7 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file --- * What is this? Someone could help me on how to fix it? Or where I can find some literature to help me? Thank you ! -- 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] problems with non pbc simulations in parallel
I'm facing the same problem, just after I became to run the molecular dynamics at i7 processor. -- 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] problems with non pbc simulations in parallel
Sorry Gavin, I didnt resolve the problem yet. I just use your question as mine too. The only thing I add was that my processor is an i7. -- 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] center peptide in simulation box
Try this: trjconv -pbc mol -ur compact And maybe you will find some useful answers here: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions I hope it helps -- Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul -- 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] Problem on i7
Hi, I'm facing a problem where the GROMACS can't distribute the job that I send between the 8 nodes of my computer (i7 920). Actually, when I send the job with the command line mpirun -np 8 mdrun (...) each CPU receive the information and perform the job by itself, without distribution. Someone that face this problem (or that know hou to fix it) could help me? Thanks !! -- 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] Problem on i7
Hi Roland, thanks for your answer. Actually, I installed the GROMACS from Synaptic package manager. I dont know if the manager compile with the --enable-mpi option. I'll try to reinstall with this option and see what happens. Thank you very much!! -- 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] Help with Segmentation fault!!!
But what is the real problem about the use of -DFLEXIBLE? Will I get wrong calculations from MD if I define it? Or it is just a matter of time (DFLEXIBLE = take longer) ?? 2010/2/18 Tsjerk Wassenaar tsje...@gmail.com Hi Deisy, define = -DFLEXIBLE integrator = md Well, probably you'd be better off with 'integrator = steep'. If you're doing MD, better not define -DFLEXIBLE. But for the rest, you give little account of what you're doing. What about the workflow, where in your scheme are we? What are you trying to do? How about some tutorial material? Cheers, Tsjerk -- 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 -- Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul -- 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] Is that true?
Hi, someone can told me if this affirmative is true for GROMACS 4.0? *The force fields and water models available for biomolecules have been developed for room temperature simulations* Or where I can find in the manual about this subject? Thanks, -- Mauricio UFRGS -- 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] Problem - can't set dodecahedrons box
Hi, I'm facing a problem with GROMACS that appears pretty simple, actually. I'm trying to set a dodecahedron box but all I can get is a triclinic box. For that, I'm using the following line: * editconf -f pMHC -bt dodecahedron -o -d 1 * Am I doing something wrong?? Another problem, different from this one, is that my protein, during the simulation, is escaping/comming off/running away (sorry I'm butchering the english) from the water box. I tried to use periodic boundaries conditions, but didn't work (I added a line in my .mdp file - pbc = xyz). Someone could help me with that, please? I really appreciate ! -- Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul - Brazil -- 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
