[gmx-users] g_mindist periodic boundary condition

[Tsjerk Wassenaar]

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 <oscarjiao at gmail.com> 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 <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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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist