Hi Dan,
Thank you for the insight. :) I agree that should yield a more consistent velocity estimate.
- Lee-Ping
> On Feb 20, 2018, at 12:36 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> On Mon, Feb 12, 2018 at 3:04 PM, Lee-Ping Wang <leeping.ucdavis.edu> wrote:
>> I want to do this because the kinetic energies that are written to “mdout” and “mden” do not correspond exactly to the written trajectory frames (i.e. mdout/mden are shifted by one frame with respect to the trajectory and velocity-trajectory). I need the kinetic energies that correspond exactly to my position trajectory frames, and it seems the only way to do this is to recompute them from the velocity-trajectory (please correct me if I’m wrong).
>
> This is only half right. Due the the leapfrog nature of the integrator
> the velocities that get written are half a time step ahead of the
> coordinates (i.e. coordinates are written at time t, velocities at
> time t+0.5*dt), so in order to get the velocities at time t you also
> need forces. I believe that one way to do this is:
>
> Vn = Vh - 0.5 * dt * Fn / m
>
> where V is velocity, n denotes time t, h denotes time n+0.5*dt, dt is
> the time step, F is force, and m is mass. However, this also will not
> be exactly what you get from sander because sander estimates Vn
> differently and depending on what thermostat you are using there are
> certain additional corrections that are used. Ultimately right now I
> think the code in runmd.F90 (and corresponding code in pmemd) is the
> only reference for how Amber estimates kinetic energy - we should
> probably develop a formal FAQ for this at some point.
>
> Other in the Amber community please correct me if I'm off base here. :-)
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Tue Feb 20 2018 - 16:00:03 PST
