Does anybody know if grompp uses the forces from a loaded .trr file in
order to create the .tpr file?
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
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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