[gmx-users] g_mindist periodic boundary condition

[Mark Abraham]

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<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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>>
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