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 <[email protected]> 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 <[email protected]> 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 <[email protected]> > > 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 [email protected] > >> 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 [email protected]. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > > gmx-users mailing list [email protected] > > 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 [email protected]. > > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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