Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12

From: Jason Swails <>
Date: Mon, 30 Mar 2015 11:34:08 -0400

On Mon, Mar 30, 2015 at 8:39 AM, Wang Moye <>

> Hello everyone!
> I have a REMD process using AMBER12. There are 26 replicas in my system.
> As the tutorial said, a typical use of REMD is to obtain thermodynamic
> ensembles at temperatures of interest (e.g. 300 K). So I extracted the
> data for each temperature . Now I want to get the potential energy for
> each temperatue , what should I do next ? I have 26 mdcrd trajectories and
> the process_mdout.perl can analyse the mdout files only.
> If I want to get the total energy and potential energy through mdcrd
> trajectories , which tool should I use ?

‚ÄčIn addition to what Christina suggested, you can also extract the energies
directly from the remlog files. I'm not sure if cpptraj does this (I know
it reads remlogs, but I'm not sure if it will extract the energies into a
data set... you could always try it and see what the manual says about it).

If you plan on using cpptraj, I suggest updating to the latest version of
AmberTools 14, as there have been numerous cpptraj improvements since Amber


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Mar 30 2015 - 09:00:04 PDT
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