On Mon, Mar 12, 2012 at 11:55 AM, David Minh <daveminh.gmail.com> 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.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Mar 13 2012 - 15:30:04 PDT
