[gmx-developers] Scaling velocities in Velocity Verlet
Shirts, Michael (mrs5pt)
mrs5pt at eservices.virginia.edu
Sat Dec 3 21:37:37 CET 2011
Hi, all-
> The problem is that the change in Ekin comes one step too late. I tried
> to deduce the algorithm from the code (4.5 code base) and deduced the
> following MD algorithm:
It's rather difficult to follow currently because of the need to bookkeep
both md and md-vv + plus correct pressure control w/constraints. I have high
hopes for improving this for 5.0.
> v(t) = v(t-dt/2) + a(t) dt/2
>
> v'(t) = lambda v(t) <======= my addition
>
> v(t+dt/2) = v'(t) + a(t) dt/2
>
> r(t+dt) = r(t) + v(t+dt/2) dt
>
> However, the Ekin that is printed is the uncorrected one even though I
> scale both ekind->ekin and ekind->tcstat[x].ekinf .
>
> Is the algorithm correct as I write it above? Is the Ekin(t) already
> stored at the beginning of the time step?
If you add your modification as an option to update_tcouple, and operate on
ekind directly (not the velocities), in the same way that berendsen_tcouple
does, then the bookkeeping should take care of the velocity rescaling
appropriately.
If this _doesn't_ work, then there's some tweaks that got lost in the
different versions that are floating around, and I can either put the
changes into 4.6 alone, or just add them in with the 4.6 merge.
Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821
> v(t) = v(t-dt/2) + a(t) dt/2
>
> v'(t) = lambda v(t) <======= my addition
>
> v(t+dt/2) = v'(t) + a(t) dt/2
>
> r(t+dt) = r(t) + v(t+dt/2) dt
>
> However, the Ekin that is printed is the uncorrected one even though I
> scale both ekind->ekin and ekind->tcstat[x].ekinf .
>
> Is the algorithm correct as I write it above? Is the Ekin(t) already
> stored at the beginning of the time step?
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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