[gmx-users] sampling the side chain conformations by MD simulations

mircial at sjtu.edu.cn mircial at sjtu.edu.cn
Sun Apr 22 08:42:48 CEST 2012

Dear All:

I am conducting molecular dynamics simulations of a proetin. The side chain conformation of one key residue is important for the protein function and I wang to sampling its conformations and calculate the energy barrier when it changes between different conformations. 

However, the common MD simulations can't sampling all of its conformations (maybe the energy barrier between different conformations is high?) and I want to enhance the sampling process. My question is does it possible to use high temperature for this residue and normal temperature for the other part of the system so that I can sample more conformations in relative short time?

I know locally enhanced sampling method maybe useful in this situation, but it seemed that it is not implemented in the GMX package.

I will be appraciate if anyone could give me some suggestions.


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