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 <jalem...@vt.edu
<mailto:jalem...@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
========================================
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