[gmx-developers] Conserved energy drifts horribly with md-vv

[Shirts, Michael R. (mrs5pt)]

> we compared the md and the md-vv integrators in single and double
>precision with the v-rescale thermostat. The md integrator does not
>conserve energy in sp but is find in dp with sufficiently short time
>steps (no constraints used anywhere). For md-vv the drift is horrible
>even in dp.

Then something someone did at some point in the integrator screwed up
md-vv, because I did pretty careful analysis of energy conservation when I
merged it in, down to checking the variance as a function of step size and
making sure it's quadratic, both with and without constraints (as did md).

The only difference should be is that vv should converge to the small-step
limit faster (less bias with increasing time step), but with more noise
than md (more noise with increasing timestep).

Unfortunately, it's incredibly easy to screw up integrators without
meaning to because of the structure of the inner loop now (cleaning that
up is one of the projects over the next few months, after grants get in at
the end of June).

I'll try to look at this over the next week or so, but will be traveling
the end of this week.


Best,
~~~~~~~~~~~~
Michael Shirts
Associate Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434) 243-1821

>
>we compared the md and the md-vv integrators in single and double
>precision with the v-rescale thermostat. The md integrator does not
>conserve energy in sp but is find in dp with sufficiently short time
>steps (no constraints used anywhere). For md-vv the drift is horrible
>even in dp. Plotted is the drift in the conserved-energy term from the
>edr file. 1000 Molecules, 1 ns.
>
>
>
>Dt(fs)  md/sp   md/dp   md-vv/sp  md-vv/dp
>2       486     501      5350      5287
>1       40      47       4915      4981
>0.5     -30     18       4769      4938
>0.25    -189    3        4306      4963
>0.1     -996    5        2496      4956
>0.05    -2783   4       -1464      4953
>
>Clues?
>-- 
>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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