[gmx-users] g_mindist output
Hi gmx users, I was running g_mindist as a batch job for a big number of files on a pbs cluster. The huge amount of output was redirected to the error file which has a size limit. Is there way to discard the output of g_mindist. I tried /dev/null as below, it didn't work. g_mindist -f tra.pdb -n tra.ndx-od log grp.txt /dev/null where grp.txt is a input file which specifies the groups. Thanks in advance. D -- 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_mindist output
Thank you, Justin. On Mon, Mar 8, 2010 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Dian Jiao wrote: Hi gmx users, I was running g_mindist as a batch job for a big number of files on a pbs cluster. The huge amount of output was redirected to the error file which has a size limit. Is there way to discard the output of g_mindist. I tried /dev/null as below, it didn't work. g_mindist -f tra.pdb -n tra.ndx-od log grp.txt /dev/null where grp.txt is a input file which specifies the groups. Use /dev/null. You can also use the -quiet flag (hidden option) to suppress some of the information printed out by any of the Gromacs tools. -Justin Thanks in advance. D -- 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] Gromacs 4.0.6 installation error
I was following the instruction to install gromacs 4.0.6 on my machine. ./configure --enable-threads --enable-float --enable-sse --prefix=[mypath] make make install The configure looks ok but no Makefile is generated. When I do make or make install, it gives me the error: make: *** No targets specified and no makefile found. Stop. There are couple makefiles in the directory though, Makefile.in and Makefile.am, do I need to rename one of them to Makefile to make it work? Dian -- 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] Gromacs 4.0.6 installation error
Actually, I tried 4.0.7 first from this link, http://www.gromacs.org/index.php?title=Download_%26_Installation It didn't work (same error). That's why I downloaded 4.0.6 from the same webpage. On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul jalem...@vt.edu wrote: Dian Jiao wrote: I was following the instruction to install gromacs 4.0.6 on my machine. ./configure --enable-threads --enable-float --|enable-sse --prefix=[mypath]| make make install The configure looks ok but no Makefile is generated. When I do make or make install, it gives me the error: make: *** No targets specified and no makefile found. Stop. There are couple makefiles in the directory though, Makefile.in and Makefile.am, do I need to rename one of them to Makefile to make it work? Per the warning on the Gromacs homepage, version 4.0.6 is a broken distribution. Use version 4.0.7 instead. -Justin Dian -- 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
Re: [gmx-users] Gromacs 4.0.6 installation error
I got it to work finally. Didn't install fftw earlier. Thanks. On Fri, Mar 5, 2010 at 4:02 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 6/03/2010 5:05 AM, Dian Jiao wrote: Actually, I tried 4.0.7 first from this link, http://www.gromacs.org/index.php?title=Download_%26_Installation It didn't work (same error). That's why I downloaded 4.0.6 from the same webpage. On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Dian Jiao wrote: I was following the instruction to install gromacs 4.0.6 on my machine. ./configure --enable-threads --enable-float --|enable-sse --prefix=[mypath]| Don't enable threads. Do follow an actual installation guide like on the GROMACS webpage. Mark make make install The configure looks ok but no Makefile is generated. When I do make or make install, it gives me the error: make: *** No targets specified and no makefile found. Stop. There are couple makefiles in the directory though, Makefile.in and Makefile.am, do I need to rename one of them to Makefile to make it work? Per the warning on the Gromacs homepage, version 4.0.6 is a broken distribution. Use version 4.0.7 instead. -Justin Dian -- 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 list gmx-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 -- 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] g_mindist periodic boundary condition
Hi Tsjerk, My gromacs is 4.0.4. As it turns out, I do not have a CRYST1 keyword in my pdb file, so I guess the box is not defined yet. The pdb was taken from the trajectory of AMBER simulation, so it starts with the keyword REMARK. How do I include box dimensions in pdb file then? Just add CRYST1 24 24 24 in the first line? By the way is it CRYST1 or CRYSTL? And the command I was running was g_mindist -f 1001.pdb -n 1001.ndx -od 1001_C. Dian On Thu, Mar 4, 2010 at 12:38 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Dian, Which version of gromacs are you using? Can you assert that the pdb file has the correct box? It should have a line starting with CRYST1 (grep ^CRYST1 file.pdb). Some versions of gromacs (3.3.2 I think) didn't write the CRYST1 record, and thus disallow PBC related operations. Cheers, Tsjerk On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao oscarj...@gmail.com wrote: The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about 31 A away from the closest water in the box. But if it is periodic, shouldn't there be waters near the dummy too? On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 4/03/2010 11:30 AM, Dian Jiao wrote: Hi Gromacs users, I was trying to compute minimum distance between groups in a cubic water box with g_mindist using periodic boundary condition. In order to test this, I added one more atom which is far away from any of the other atoms in the pdb file. The mindist between that atom and all the waters were computed. The output of g_mindist is 3.089281e+00. (the unit is nm, right?) You haven't said how big your box is, or how far far away is, so we can't tell whether you think 3nm is too big, too small, etc. The manual shows that pbc is one of the option of g_mindist, but isn't the default yes? I even tried with -pbc in the command, still did not work. Can anyone tell me how to turn on PBC in g_mindist? See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off. 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 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 -- 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 -- 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_mindist periodic boundary condition
Sorry for the confusion, Tsjerk. Thanks. On Thu, Mar 4, 2010 at 11:47 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Dian, Now why didn't I guess that you were trying on data obtained from Amber?! Maybe because you didn't explicitly mentioned it. It always helps to give a full account of what you were trying. Anyway, I don't know the format of the top of my head, so you'll have to look in another pdb file and copy/edit the line (I think it's angles and then lengths, all %8.3f, but I'm not sure), or you have to check the pdb format at www.rcsb.org/pdb Hope it helps, Tsjerk On Thu, Mar 4, 2010 at 6:04 PM, Dian Jiao oscarj...@gmail.com wrote: Hi Tsjerk, My gromacs is 4.0.4. As it turns out, I do not have a CRYST1 keyword in my pdb file, so I guess the box is not defined yet. The pdb was taken from the trajectory of AMBER simulation, so it starts with the keyword REMARK. How do I include box dimensions in pdb file then? Just add CRYST1 24 24 24 in the first line? By the way is it CRYST1 or CRYSTL? And the command I was running was g_mindist -f 1001.pdb -n 1001.ndx -od 1001_C. Dian On Thu, Mar 4, 2010 at 12:38 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Dian, Which version of gromacs are you using? Can you assert that the pdb file has the correct box? It should have a line starting with CRYST1 (grep ^CRYST1 file.pdb). Some versions of gromacs (3.3.2 I think) didn't write the CRYST1 record, and thus disallow PBC related operations. Cheers, Tsjerk On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao oscarj...@gmail.com wrote: The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about 31 A away from the closest water in the box. But if it is periodic, shouldn't there be waters near the dummy too? On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 4/03/2010 11:30 AM, Dian Jiao wrote: Hi Gromacs users, I was trying to compute minimum distance between groups in a cubic water box with g_mindist using periodic boundary condition. In order to test this, I added one more atom which is far away from any of the other atoms in the pdb file. The mindist between that atom and all the waters were computed. The output of g_mindist is 3.089281e+00. (the unit is nm, right?) You haven't said how big your box is, or how far far away is, so we can't tell whether you think 3nm is too big, too small, etc. The manual shows that pbc is one of the option of g_mindist, but isn't the default yes? I even tried with -pbc in the command, still did not work. Can anyone tell me how to turn on PBC in g_mindist? See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off. 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 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 -- 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 -- 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 -- 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 -- gmx-users mailing listgmx-users@gromacs.org http
[gmx-users] g_mindist periodic boundary condition
Hi Gromacs users, I was trying to compute minimum distance between groups in a cubic water box with g_mindist using periodic boundary condition. In order to test this, I added one more atom which is far away from any of the other atoms in the pdb file. The mindist between that atom and all the waters were computed. The output of g_mindist is 3.089281e+00. (the unit is nm, right?) The manual shows that pbc is one of the option of g_mindist, but isn't the default yes? I even tried with -pbc in the command, still did not work. Can anyone tell me how to turn on PBC in g_mindist? Thanks Dian -- 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_mindist periodic boundary condition
The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about 31 A away from the closest water in the box. But if it is periodic, shouldn't there be waters near the dummy too? On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/03/2010 11:30 AM, Dian Jiao wrote: Hi Gromacs users, I was trying to compute minimum distance between groups in a cubic water box with g_mindist using periodic boundary condition. In order to test this, I added one more atom which is far away from any of the other atoms in the pdb file. The mindist between that atom and all the waters were computed. The output of g_mindist is 3.089281e+00. (the unit is nm, right?) You haven't said how big your box is, or how far far away is, so we can't tell whether you think 3nm is too big, too small, etc. The manual shows that pbc is one of the option of g_mindist, but isn't the default yes? I even tried with -pbc in the command, still did not work. Can anyone tell me how to turn on PBC in g_mindist? See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off. 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 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
