[gmx-users] (no subject)

[Mark Abraham]

Hi,

On Wed, Jun 21, 2017 at 4:32 PM Shivangi Agarwal <
shivangi.agarwal800 at gmail.com> wrote:

> Hi
> But it is broken. ..
>

Nope, it's just in one of the infinite number of equivalent representations
of the same thing ;-) mdrun doesn't know that you want it to write a file
where your protein and ligand and whatever strand are a cluster of things
that you'd like it to render centered in the same periodic cell. That's
what e.g. gmx trjconv -pbc cluster is useful for.

strand with proline with three odr residues has been broken and visible...
> i have Checked in vmd and pymol
>

Doesn't matter until you've said to a program "keep these things together"
:-)

Mark


> On 21 Jun 2017 17:16, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>
> > Hi,
> >
> > On Wed, Jun 21, 2017 at 1:21 PM Shivangi Agarwal <
> > shivangi.agarwal800 at gmail.com> wrote:
> >
> > > Hello to all gmx users
> > >
> > > I am performing protein ligand complex MD simulation but my protein
> > > structure has been broken during energy minimization process.
> > >
> >
> > It's not broken, but rather in an unexpected representation. See
> > http://www.gromacs.org/Documentation/Terminology/
> > Periodic_Boundary_Conditions
> > for
> > background and suggestions.
> >
> > Mark
> >
> >
> > > What may be the suitable reason? How I can solve this?
> > > Your support is highly appreciated
> > > --
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