[gmx-users] REMD As A Function of Distance Between 2 Chains

Huey Ling Tan huelyn at gmail.com
Mon Nov 12 19:24:14 CET 2007

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.ppafiles 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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