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

Mu Yuguang (Dr) YGMu at ntu.edu.sg
Tue Nov 13 00:39:15 CET 2007

Dear Huey Ling,

In principle it is applicable. Then such REMD can be termed as
Hamiltonian REMD instead of canonical temperature REMD.


Dr. Yuguang Mu

School of Biological Sciences

60 Nanyang Drive 

Nanyang Technological Uiversity


Tel: +65-63162885



From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Huey Ling Tan
Sent: Tuesday, November 13, 2007 2:24 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] REMD As A Function of Distance Between 2 Chains


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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