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.
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