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
--
========================================
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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