[gmx-users] Velocity Verlet integrator

[Justin Lemkul]

On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
> Dear all,
>
> I am still interested in some integrator related issues.
>
> I understand that the easiest way to implement velocity Verlet was to split
> the updates in two updates. But I don't understad the order of those
> updates.
> I mean why there are two updates for velocities and then the update for
> positions?
> My intuitive idea would be to update first one half for velocities, then a
> full step for positions and, finally, using these new positions the second
> half for velocities.

Yes, there are two separate half-step updates for velocities.  The comments in 
the md.cpp code are quite verbose if you want to trace through.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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