[gmx-users] REMD simulation of peptide-membrane system

[Mark Abraham]

On 03/03/11, Jianguo Li  <ljggmx at yahoo.com.sg> wrote:
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> Dear all,
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> 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:
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> (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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