[gmx-users] lipid-protein simulation

[Justin Lemkul]

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

-- 
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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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