Re: [AMBER] Energy and Coordinate Outputs

From: Jason Swails <>
Date: Tue, 13 Mar 2012 18:22:11 -0400

On Mon, Mar 12, 2012 at 11:55 AM, David Minh <> wrote:

> Hi David,
> Thanks for the suggestions.
> It looks like ntpr and ntwe (energies) are one time step off from ntwx
> (coordinates) in AMBER 11. If I do a 100 step trajectory outputting
> energies and coordinates at each step, the 100th energy output from the
> trajectory corresponds to the 99th coordinate set. But it looks like
> pmemd.cuda and sander energies are pretty close, so I will just run
> pmemd.cuda trajectories through sander to get the gb and pbsa energies.

The 1-time-step-off is expected. The workflow in the MD routine is this:

1. calculate energies and forces on the current structure
2. propagate dynamics
3. If printing, print the structure and the energies (Do _not_ recalculate
the energy)

>From this ordering, you can see that the calculated energy corresponds to
the conformation prior to the coordinate update (propagated dynamics). If
you follow this in a cycle, you will see that the energies for each step
correspond to the structure that was printed the step before, leading to
this offset that you observe.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Mar 13 2012 - 15:30:04 PDT
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