[gmx-users] Simulations of proteins in membrane bilayer

[Catarina A. Carvalheda dos Santos]

Hey,

If that doesn't do the trick use the flags suggested by Terry and also '-ur
compact'. This works for me.

Regards,

On 1 October 2015 at 02:49, Terry <terrencesun at gmail.com> wrote:

> Hi,
>
> Try options '-pbc mol -center' with the gmx trjconv tool.
>
> Terry
>
>
> On Thu, Oct 1, 2015 at 4:48 AM, 凌未风 <grx1985 at qq.com> wrote:
>
> > Hi All:
> >
> > I am doing a simulation in which a protein is inserted into a bilayer. In
> > my simulations, the protein moved on the x-y plane of the bilayer (which
> is
> > normal). However, in order to do some analysis, I have to put the protein
> > to the center of the box, but still keep the box filled by lipids. Does
> > anyone know how to do this?
> > Of course, I could put the protein to the center of the box by align the
> > protein with that in the first snapshot, but in this way, some of the
> > lipids will be out of the PBC box. In my case, I have to keep all of the
> > lipids in the PBC box and packed around the protein.
> >
> > I am really appreciate for your suggestions and help.
> >
> > With my best regards,
> > RXG
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-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
School of Life Sciences
University of Dundee
DD1 5EH, Dundee, Scotland, UK