<div>There was a typo in the mail:</div>E_protein-protein = Potential - E_water-water - E_protein-water<br><br><div class="gmail_quote">On Mon, Mar 28, 2011 at 11:55 AM, Sai Pooja <span dir="ltr"><<a href="mailto:saipooja@gmail.com">saipooja@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi,<div><br></div><div>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:</div>
<div><br></div><div>For the nth replica:</div>
<div><br></div><div>E_n = E_protein-protein + a_n * E_protein-water + b_n * E_water-water</div><div><br></div><div>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.</div>
<div><br></div><div>E_water-water = LJ_water-water + Coulomb_water-water</div><div>E_protein-water = LJ_protein-water + Coulomb_protein-water</div><div>E_protein-protein = Potential - E_protein-protein - E_protein-water</div>
<div><br></div><div>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.</div>
<div><br></div><div>Pooja</div><div><br></div><font color="#888888"><div><br></div><div><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>