On Thu, Apr 2, 2015 at 4:49 PM, Brian Radak <brian.radak.accts.gmail.com>
wrote:
> Is there a reason the write to disk has not been moved? Is it just legacy
> purposes?
I'm not sure if that's the only reason, but it's certainly a
consideration. This has been the behavior for the better part of 2 decades
as far as I know (possibly longer).
> I don't understand the specific utility in *not* having the
> energies match. I know there is a slight difficulty with the kinetic energy
> (which is a result of leapfrog), does that confuse things?
>
You can get the velocities at the same timesteps as the coordinates by
averaging the half time-step before and after (and this is what is done to
make sure that the kinetic energy reported is given for the same time step
as the energies are in the mdout file.
You lose a little accuracy in the kinetic energy by doing this, but I think
the error is still only of the order of dt^-3 (maybe dt^-2, I'd have to
review the leapfrog derivation).
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Apr 03 2015 - 07:30:02 PDT
