[gmx-users] Re: Resplica exchange with solute tempering (REST)
saipooja at gmail.com
Mon Mar 28 19:54:16 CEST 2011
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 <saipooja at gmail.com> wrote:
> 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.
> Quaerendo Invenietis-Seek and you shall discover.
Quaerendo Invenietis-Seek and you shall discover.
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