Re: [AMBER] post processing temperature replica exchange trajectories

From: Jason Swails <>
Date: Fri, 20 Mar 2015 08:24:02 -0400

On Thu, Mar 19, 2015 at 4:00 PM, Sandeep Somani <> wrote:

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

​Just one other comment -- the energies are in the REMD log file. They're
somewhat lower precision than what sander prints out (to the hundredths
rather than ten-thousandths place), but should be good for many

cpptraj *does* have the ability to read in and analyze REMD log files (not
sure if this applies to energies as well).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 20 2015 - 05:30:08 PDT
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