[gmx-users] Simulations of proteins in membrane bilayer

Terry terrencesun at gmail.com
Thu Oct 1 03:49:25 CEST 2015


Try options '-pbc mol -center' with the gmx trjconv tool.


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,
> --
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