[gmx-users] g_mindist periodic boundary condition

[Tsjerk Wassenaar]

Hi Dian,

Now why didn't I guess that you were trying on data obtained from
Amber?! Maybe because you didn't explicitly mentioned it. It always
helps to give a full account of what you were trying.

Anyway, I don't know the format of the top of my head, so you'll have
to look in another pdb file and copy/edit the line (I think it's
angles and then lengths, all %8.3f, but I'm not sure), or you have to
check the pdb format at www.rcsb.org/pdb

Hope it helps,

Tsjerk

On Thu, Mar 4, 2010 at 6:04 PM, Dian Jiao <oscarjiao at gmail.com> wrote:
> Hi Tsjerk,
>
> My gromacs is 4.0.4.
>
> As it turns out, I do not have a CRYST1 keyword in my pdb file, so I guess
> the box is not defined yet. The pdb was taken from the trajectory of AMBER
> simulation, so it starts with the keyword "REMARK". How do I include box
> dimensions in pdb file then? Just add "CRYST1 24 24 24" in the first line?
> By the way is it CRYST1 or CRYSTL?
>
> And the command I was running was "g_mindist -f 1001.pdb -n 1001.ndx -od
> 1001_C".
>
> Dian
>
> On Thu, Mar 4, 2010 at 12:38 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> 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.
>>
>> 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
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist