[gmx-users] GridMatMD and CGMD

[Justin A. Lemkul]

Anirban Ghosh wrote:
> Hello Justin,
> 
> Thanks for the reply.
> Actually I am using the last frame .gro of a 3 micro-second run CGMD 
> simulation as the input for GridMatMD. But in the thickness plot the 
> positions of the protein depicted are not matching with what I am 
> visualizing through VMD. I suppose this is because of some PBC issue. 
> What -pbc options should I use to generate a proper .gro file to be used 
> as input for GridMatMD?

The input for GridMAT-MD does not necessarily need to be whole.  I can't tell 
what the problem is from this description.  What doesn't match?  How different 
are the results?

-Justin

> Thanks a lot again.
> 
> Regards,
> 
> Anirban
> 
> On Mon, May 30, 2011 at 4:40 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
>     Anirban Ghosh wrote:
> 
>         Hi ALL,
> 
>         I have simulated a CGMD system consisting of multiple copies of
>         a CG protein in a CG lipid bilayer using the MARTINI FF for the
>         CG definitions. Can I use GridMatMD program to calculate the
>         area per lipid and other properties in this CG system? Which
>         parameters do I need to alter in the input file for GridMatMD in
>         order to properly recognize the CG lipids?
> 
> 
>     CG lipids should work like any other - specify their name in the
>     input file, and the atom name that should be used as a reference
>     point.  We have never tested GridMAT-MD with a CG membrane, but it
>     should work the same way as an atomistic membrane.  Please let me
>     know if you encounter any problems.
> 
>     -Justin
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================