On 9/16/12 12:48 PM, Shima Arasteh wrote:
Thanks.
Yes, I want to use the coordinate file from 50-ns simulation. Would you please
let me know what the criterion for knowing that the equilibrated system is
proper for insertion of protein? Do the temperature, RMSD, pressure and
visualization of popc-water system make me decide that it is a proper system or
not?
None of those criteria are specific enough, in my opinion. Lipid-specific
metrics like area per lipid, membrane thickness, lateral diffusion, etc should
all be considered. There is a wealth of literature that exists about membrane
simulations from which you can draw ideas.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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