[gmx-developers] Question on -rerun

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Mon Dec 31 05:59:40 CET 2012

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.


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
* 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

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.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

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