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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Jan 30 20:19:49 CET 2008

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:  

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."


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