[gmx-users] Re: Resplica exchange with solute tempering (REST)

Sai Pooja saipooja at gmail.com
Tue Mar 29 19:29:59 CEST 2011

It is working. The error was clerical. Thank you for your time.

On Tue, Mar 29, 2011 at 10:52 AM, Sai Pooja <saipooja at gmail.com> wrote:

> On Mon, Mar 28, 2011 at 6:39 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>>  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 <saipooja at 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.
> 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.
> 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?
> Mark
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> Quaerendo Invenietis-Seek and you shall discover.

Quaerendo Invenietis-Seek and you shall discover.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110329/8fa3cf2d/attachment.html>

More information about the gromacs.org_gmx-users mailing list