[gmx-users] Re: Folding rate

[Mark Abraham]

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