[gmx-developers] Question on -rerun

Berk Hess hess at kth.se
Mon Dec 31 13:31:08 CET 2012


My opinion is that all potential energies and forces should be reproduced.
With velocities in the trr the velocities, kinetic energy, temperature, 
and pressure should not be far off, as the temperature coupling should
only have a minor effect within one step. I don't think a user would care
about the last few decimals being different.
We can simply note in the manual that all velocity dependent quantities
are not present (or unreliable) without velocities and can be slightly off
by as much as the T-coupling effect in one step when v is present.



On 12/31/2012 05:59 AM, Shirts, Michael (mrs5pt) wrote:
> Hi all-
> I'm double checking free energy behavior under -rerun; more a
> clarification/discussion  question than a bug, so I'm emailing the
> developers list.
> What's the official policy on what the -rerun flag can reproduce or not from
> the original trajectory if both x and v are specificed in the trajectory?  I
> poked around on the mailing list a bit, and couldn't get a consistent
> answer. The manual says "forces and energies" I've talked a bit with Berk
> about this, but that was a couple of years ago, and I'm not sure if
> everything was really finalized.  It could be that this has all been
> discussed before, but it's not really talked about in the manual.
> So:
> Things that should be definitely be reproduced (and appear to be, once I
> check in a couple of bug fixes for md-vv)
> * potential energies and forces
> * velocities and temperature (any NVE integrator, also md-vv for NVT and
> NPT)
> * pressure and virial (any NVE integrator)
> Things that are not clear are necessarily reproduced (and definitely are not
> always reproduced in the current code)
> * velocities and temperature (md for NPT and NVT)
> * pressure, virial (any NPT or NVT integrator)
> For example, currently, if NoseHoover thermostat is used with the md
> integrator, then the kinetic energies will not be correct, as the velocity
> rescaling history is lost in the -trr rerun.
> There are two main issues:
> 1) There are auxiliary integrator variables that are not saved in .trrr and
> 2) for md, an integration step taken in between when the coordinates are
> printed out and when the .edr file is generated, so any integrator auxiliary
> variables are eliminated. I wonder if we should think about reorganization
> of this in 5.0, though I'm not sure it's even possible, since for md, you
> need both half-step velocities, and hence you have to take an integration
> step.
> So for 4.6, it seems like the best thing may be to put more warnings in the
> manuals, as well as in the output -- right now it only warns about kinetic
> energies, temperatures and pressures if there are velocities frames missing
> from the trajectory.
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821

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