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

Justin A. Lemkul jalemkul at vt.edu
Mon May 7 14:35:02 CEST 2012

On 5/7/12 1:01 AM, Anirban Ghosh wrote:
> On Mon, May 7, 2012 at 10:17 AM, Bala S <think_beyond at aol.com
> <mailto: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).

I have always found the VMD method to be hit-or-miss and often frustrating.  It 
is also possible to use the -center option of editconf to position the protein 
of interest at a given location, and/or use -translate or -rotate.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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