[gmx-users] REMD As A Function of Distance Between 2 Chains
Huey Ling Tan
huelyn at gmail.com
Wed Nov 14 16:23:01 CET 2007
Dear all ,
thank you for those comments, we are aware of the paper. However, we are
not sure how to implement the replica exchange in gromacs. We would like to
run a set of replicas in which each replica corresponds to a different set
of umbrella parameters. However, when setting up a replica exchange run,
all .tpr files use the same .ppa file so that each replica will have the
same umbrella potential parameters. Do you know how to get around this
Thank you in advance,
On 13/11/2007, Marcus Kubitzki <mkubitz at gwdg.de> wrote:
> Hi Huey Ling,
> have a look at Y.Sugita et al. J Chem Phys 113, 6042-6051 (2000) for
> details on Hamiltonian REMD, especially the correct exchange criterion.
> In their paper, they discuss in detail what you want to do, namely
> Replica Exchange Umbrella Sampling.
> Huey Ling Tan wrote:
> > Hi all,
> > Is it feasible to do parallel tempering (replica exchange) as a function
> > of distance with umbrella sampling applied?
> > I can do REMD for a system containing 2 peptide chains as a function as
> > temperatures, where I grompp each of the systems at different
> > temperatures, and then gather the fullmd.tpr files in one folder with
> > the script I want for full md run.
> > But what if I want to do REMD as a function of distances (for example at
> > 0.4, 0.6, 0.8, 1.0 nm between the chains, defined in the pull.ppa file),
> > at a fixed temperature, with umbrella sampling applied? If this can be
> > done, how should I write the script for the full md run so that each of
> > the pull.ppa files can recognise the system that it suppose to pull?
> > If anyone know how this can be done?
> > Many thanks.
> > --
> > Best regards,
> > Huey Ling
> > ------------------------------------------------------------------------
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> Marcus Kubitzki
> Max Planck Institute for Biophysical Chemistry
> Computational Biomolecular Dynamics Group
> Am Fassberg 11
> D-37077 Göttingen
> phone: ++49-551-2012312
> fax: ++49-551-2012302
> Email: mkubitz[at]gwdg.de
> www: http://www.mpibpc.mpg.de/groups/de_groot/
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