Re: [AMBER] post processing temperature replica exchange trajectories

From: Daniel Roe <>
Date: Thu, 19 Mar 2015 20:57:03 -0600


On Thu, Mar 19, 2015 at 2:00 PM, Sandeep Somani <> wrote:
> 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

Seems fine - by the way you can also read those mdout files directly
into cpptraj or, so you may be able to skip the

> This works, but the sander step is quite slow.

If you've got access to a multi-core machine you should be able to use
the MPI version of sander for some speedup here.

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

Unfortunately no, not exactly. The integration scheme results in the
energies and coordinates being offset by a timestep. The way that
you're doing it is the best way to obtain the exact energies from your
coordinates (especially for replica trajectories).

> Is there a cpptraj command for this?

There will be a command in the upcoming cpptraj release, 'energy',
which will allow the computation of simple energy terms (bond, angle,
dihedral, vdw + electrostatic with no PBC) but for other energy terms
(gb, PME nonbond) sander is still your best bet.


> Or does anyone have a script to share? :-)
> Thanks in advance!
> Sandeep
> ---
> Sandeep Somani
> Discovery Sciences
> Janssen R&D
> Spring House PA
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Mar 19 2015 - 20:00:03 PDT
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