On Mon, Mar 28, 2011 at 6:39 PM, Mark Abraham <mark.abra...@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 <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. > > 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@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Quaerendo Invenietis-Seek and you shall discover.
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