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 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
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