On 03/03/11, Jianguo Li <ljg...@yahoo.com.sg> wrote:
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> Dear all,
>
> I'd like to do folding simulations of a short peptide on membrane surface
> using REMD using atomistic FF. But the problem is that membrane will disrupt
> at high temperatures. To maintain the membrane structure, I am thinking the
> following two methods:
>
> (1) To use different coupling temperature for different groups (e.g., keeping
> membrane at 323K for all the replicas, but keeping peptide and water with
> different temperatures). Will this lead to artifact?
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Yes. You will have heat flowing via the system between two external heat baths.
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> (2) If this leads to serious artifact, I may need to use constraints on the
> membrane, as mentioned in the paper from Berkowitz group.
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That seems more wise, but still not great.
Mark
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