[gmx-users] Simulations of proteins in membrane bilayer

[Terry]

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>