Thank you David and Jason for replying and elaborating on this!
On Mar 13, 2012, at 6:22 PM, Jason Swails wrote:
> 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 Sat Mar 17 2012 - 05:30:03 PDT
