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

Jianguo Li ljggmx at yahoo.com.sg
Thu Mar 3 09:42:35 CET 2011

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? 

(2) If this leads to serious artifact, I may need to use constraints on the 
membrane, as mentioned in the paper from Berkowitz group.

Is there any other method for the above problem?

Any comments is greatly appreciated, thank you in advance,


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