[gmx-users] g_mindist periodic boundary condition

[Dian Jiao]

Sorry for the confusion, Tsjerk. Thanks.

On Thu, Mar 4, 2010 at 11:47 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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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> >> >
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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
> --
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