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-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
