[gmx-developers] does grompp utilize forces from .trr files

[David van der Spoel]

chris.neale at utoronto.ca wrote:
> Does anybody know if grompp uses the forces from a loaded .trr file in
> order to create the .tpr file?
no

> 
> My interest is based on the fact that trjconv does not appear to
> deshuffle forces as it does for coordinates and velocities as
> presented in a recent gromacs thread starting here:
> http://www.gromacs.org/pipermail/gmx-users/2008-January/031970.html
does shuffling work correctly with the -force flag?
> 
> Since I do use shuffle and use grompp-based restarts using the .trr,
> .edr, and proper gen_vel + unconstrained_start settings I am wondering
> if this has affected my runs at all. My now-fortuitous ignorance of
> the -force option to trjconv means that the .trr files that i passed
> to grompp simply did not have any forces (instead of having improperly
> ordered forces).
> 
> I took a look at the manual and there is no indication that grompp
> actually uses the force information from the .trr (on the pages that I
> looked at), but still it would be nice to have some confirmation.
> 
> I also note that I am not particularly concerned because even if
> forces are taken from the .trr by grompp, I doubt that the absence of
> forces for one step every 50-200ps is a larger perturbation than
> regenerating velocities on that timescale via gen_vel=yes, which I do
> not believe would affect equilibrium properties.
> 
> Quoting page 252 of the 3.3 manual:
> 
> "Starting coordinates can be read from trajectory with -t. The last
> frame with coordinates and velocities
> will be read, unless the -time option is used. Note that these
> velocities will not be used when gen vel =
> yes in your .mdp file. An energy file can be supplied with -e to have
> exact restarts when using pressure
> and/or Nose-Hoover temperature coupling. For an exact restart do not
> forget to turn off velocity generation
> and turn on unconstrained starting when constraints are present in the
> system. If you want to continue a
> crashed run, it is easier to use tpbconv."
> 
> Thanks,
> Chris.
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se