On 4/01/2012 12:35 PM, bharat gupta wrote:
Thanks for all your replies. I want to know this can be done in
gromacs or not - using REMD with structure based models generated from
SMOG server to study protein folding and unfolding ??.
Well, it can be done, but you probably don't have enough computer to
fold a 230 residue protein at atomistic resolution (or maybe even
coarse-grained).
Also, I have a question about how to determine the exchange
probablities for a particular REMD experiment and also how many
replicas do we need to consider, does that depend on the temperature
list generated from the T_REMD server??
There's a significant literature on these subjects. I suggest you read
some of it. Short answer: pick the highest temperature according to the
size of the largest barrier you expect to cross (good luck guessing
that), have around 20% exchange acceptance, and be prepared to observe
where the replica-flow bottle necks are and to iteratively refine you
temperatures.
Mark
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