Is there a reason the write to disk has not been moved? Is it just legacy
purposes? 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?
On Thu, Apr 2, 2015 at 3:12 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Apr 2, 2015 at 3:06 PM, Brian Radak <brian.radak.accts.gmail.com>
> wrote:
>
> > Can you actually do that or are you off by the 1 time step as usual due
> to
> > leapfrog? This appears to still be the case with amdlog files too.
> >
> > I would likely accept the argument that the difference is below
> statistical
> > error, but the imin = 5 solution is guaranteed to be correct and not
> > particularly expensive, especially if your print step is 10^3-10^4 times
> > larger than your time step.
> >
>
> ​True, the trajectories are 1 timestep off (but not because of leapfrog --
> it's because the snapshots are printed after they are propagated; this
> could easily be fixed by moving the trajectory write *before* the
> propagation step). If you need the energies to correspond to the snapshots
> in the trajectory (rather than just a time series of energies), the imin=5
> solution is what you need to do.
>
> Thanks for the catch,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
--
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak.uchicago.edu
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Received on Thu Apr 02 2015 - 14:00:02 PDT
