[gmx-users] a question related to REMD

[Justin A. Lemkul]

Acoot Brett wrote:
> 
> Dear All,
> 
> In "http://www.gromacs.org/Documentation/How-tos/REMD", the first 
> sentence is "Replica-Exchange Molecular Dynamics (REMD) is a technique 
> used to enhance sampling relative to a standard molecular dynamics 
> simulations 
> <http://www.gromacs.org/Documentation/Terminology/Molecular_Dynamics_Simulations> 
> by allowing systems of similar potential energies to sample 
> conformations at different temperatures. By doing so, energy barriers on 
> the potential energy surface might be overcome, allowing for the 
> exploration of new conformational space."
> 
> It sepcifically mentioned "by allowing systems of similar potential 
> energies to sample conformations at different temperatures". What I want 
> to know is that at different temperature, protein can have extremely 
> different potential energies, thus how the REMD gurantees "similar 
> potential energies"?
> 

The potential energy is calculated for each system from all the normal equations 
and then a probability of exchange is calculated at the exchange interval 
according to the equation given in manual section 3.13.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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