Re: [gmx-users] g_mindist periodic boundary condition
On 4/03/2010 6:38 PM, Tsjerk Wassenaar 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. Also, always copy and paste your actual command lines, so that we know what you've actually done, rather than filtering a description through your head and then adding our assumptions. Does -pbc vs -nopbc make a difference? Mark On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiaooscarj...@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 Abrahammark.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 -- 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
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 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 -- 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 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 -- 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] 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
[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
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
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
Re: [gmx-users] g_mindist periodic boundary condition
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 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 -- 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
