<br><br><div class="gmail_quote">On Mon, Mar 28, 2011 at 6:39 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff">
On 29/03/2011 4:54 AM, Sai Pooja wrote:
<blockquote type="cite">
<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" target="_blank">saipooja@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);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>
</blockquote>
</div>
</blockquote>
<br>
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.<br>
<br></div></blockquote><div> </div><div>I have almost the same no. of molecules in the system (503 in my simulation vs 512 in the paper). I change the combination rule to '1' in the forcefield.itp file, convert sigma and epsilon to C6 and C12 in ffnonbonded files, scale the epsilon according to the potential energy scaling for LJ potential and use tables with scaled coulomb interactions. User and Cutoff are specified respectively for Coulomb and Vdw interactions in the mdp file.</div>
<div><br></div><div>I guess I dont need convert sigma and epsilon to C6 and C12 since I am not using tables for the LJ potential. However, since the combination rule and the C6, C12 values are consistent, that shouldnt be a problem?</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff">
Mark<br>
</div>
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