[gmx-users] g_mindist periodic boundary condition

Dian Jiao oscarjiao at gmail.com
Thu Mar 4 08:08:25 CET 2010

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 <Mark.Abraham at anu.edu.au>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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