[gmx-users] g_mindist periodic boundary condition

[Dian Jiao]

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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