[AMBER] post processing temperature replica exchange trajectories

From: Sandeep Somani <ssomani.gmail.com>
Date: Thu, 19 Mar 2015 16:00:49 -0400


I am interested in extracting the energy values corresponding to a given
temperature from a (implicit solvent) temperature replica exchange
I am currently doing this as follows:
1. use ensemble keyword of cpptraj to extract trajectories for each
2. process each trajectory via sander using imin=5
3. grep out energy values from the generated mdout files

This works, but the sander step is quite slow.

I think the same information can be extracted from the original mdout files
and rem.log file.

Is there a cpptraj command for this?
Or does anyone have a script to share? :-)

Thanks in advance!


Sandeep Somani
Discovery Sciences
Janssen R&D
Spring House PA
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Received on Thu Mar 19 2015 - 13:30:02 PDT
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