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 >
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