[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

On Mon, May 7, 2012 at 10:17 AM, Bala S <think_beyond at aol.com> wrote:

> Justin and Anirban,
>
> I have another query on membrane simulation following your tutorials.
>
> How do I insert only a part of protein into the lipid bilayer and carryout
> the simulation?
>

editconf with -box option helps you to orient your protein with respect to
the bilayer. And visually in VMD you have the option of move a "molecule"
under "mouse" option in which you can move your protein wrt the bilayer
(when the bilayer and the protein .gro/.pdb files are loaded separately in
VMD).

-Anirban


>
> Thanks
> Bala S
>
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