[gmx-users] GridMatMD and CGMD

[Anirban Ghosh]

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?
Thanks a lot again.

Regards,

Anirban

On Mon, May 30, 2011 at 4:40 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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