On 29/03/2011 4:54 AM, Sai Pooja wrote:
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
<mailto: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.
The exchange ratio depends on the overlap integral of the distributions
of the potential energy. To have a chance of reproducing their work,
you need to use similar numbers of degrees of freedom (i.e. number of
atoms) so that the ratio of width/average of your distributions is similar.
Mark
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