sunny mishra wrote:
Hi Justin,
Thanks for the expedient reply. In the MARTINI tutorial they have
provided two water.gro files one for lipids and the other for
proteins. Protein water molecule file consists of 10800 atoms of water
and the lipid has 400 atoms. So even if I simulate any protein
structure after converting that to CG, can I use the same water.gro
file for protein always?
I don't know about different water files based on the system; that seems a bit
arbitrary. I'm referring to the one single water.gro file here:
http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html
If there are differences between using the water structure with proteins and
lipids, any changes are likely reflected in the force field, version 2.0 for
lipids, and version 2.1, which is the extension to proteins, if there is a
difference at all. Any reasonable equilibrated box of water will probably
suffice; your equilibration will likely take care of any differences, if they exist.
-Justin
Sunny
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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