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
