replica exchange trajectories

From: Raul Alcantara (
Date: Fri Nov 23 2007 - 13:12:48 CST

Hello NAMD developers and users...

I have been playing with the replica exchange example of NAMD.... From
what I can tell the implementation switches temperatures between
simulations instead of switching coordinates (which makes a lot of
sense, since its far easier to communicate one number vs. an array of
coordinates). However the output trajectories won't conform to an NVT
ensemble since they contain snapshots with different temperatures. One
would only have to re-sort all the output snapshots according to
temperature to fix this problem.

Since I'm kind of TCL deficient... I was wondering if somebody had
already written a script to do something similar to this?

Thank you...

Raul Alcantara
Computational Biochemistry and Biophysics lab
Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
Parc de Recerca Biom├Ędica de Barcelona

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