There was a typo in the mail: E_protein-protein = Potential - E_water-water - E_protein-water
On Mon, Mar 28, 2011 at 11:55 AM, Sai Pooja <saipo...@gmail.com> wrote: > Hi, > > I have tried to implement a variant of Replica exchange called REST using > gromacs. In REST, the potential energy is scaled in the following manner: > > For the nth replica: > > E_n = E_protein-protein + a_n * E_protein-water + b_n * E_water-water > > I used tables to implement this. Separate tables for the three components > were generated with the corresponding scaled potentials. Then for replica > exchange I use gromacs to run MD for 1ps then extract the Energy > corresponding to the three components using g-energy and exchange replicas > based on the acceptance criteria outlined in the paper. > > E_water-water = LJ_water-water + Coulomb_water-water > E_protein-water = LJ_protein-water + Coulomb_protein-water > E_protein-protein = Potential - E_protein-protein - E_protein-water > > Is there some obvious error in this implementation? I use CHARMM forcefield > with tip3p water and alanine dipeptide. The paper uses OPLS-AA with tip4p > and is able to use 3 replicas -300k, 420k, 600k. I am not able to reproduce > these results i.e. the same acceptance ratio with 3 replicas. 5 replicas > gives something close to the desired acceptance ratio. > > Pooja > > > > > -- > Quaerendo Invenietis-Seek and you shall discover. > -- Quaerendo Invenietis-Seek and you shall discover.
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