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

[chris.neale at utoronto.ca]

Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> 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

Thanks, I am happy to hear that.

>
>>
>> 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?

No. Without the -force flag, forces are not output at all. With the  
-force flag, they are out but they are not affected by the -n option  
to tpbconv. I posted a possible fix here and some very simple testing:
http://www.gromacs.org/pipermail/gmx-users/2008-January/031993.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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>
>
> -- 
> 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
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