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.
Marcus
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
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D-37077 Göttingen
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