[gmx-users] how to set "gen_vel" in mdp file and continue a crashed run

Xavier Periole x.periole at rug.nl
Tue May 24 10:54:07 CEST 2005

> 1. "gen_vel=yes" with "gen_temp=ref_t" (ref_t for T-coupling) will 
> speed up equilibration slightly.
David certainly meant by equilibration the sampling issue of MD. If you 
generate new velocities
you begin a new simulation. It would not be correct to consider it as 
the continuation of the first one.

> 2. for a new simulation, "gen_vel=yes" should be set for PR-MD, and 
> "gen_vel=no" for the final MD, velocities at t=0 will be read from the 
> gro file;
> for a continuation md simulation, "gen_vel=no" should be set, 
> otherwise you start a new simulation from the structure or 
> conformation of the previous simulation.

that is right.

> 3. to continue a complete run, just using the final gro and 
> "gen_vel=no"; or use tpbconv with -until or -extend option.

> 4. to continue a crashed run with tpbconv, gen_vel does not influence 
> because velocity will be read from trr file.

> to continue a crashed run, with T, P coupling
> set in mdp file, eg. "nstxout=10000" and "nstvout=10000"
> # check the last complete frame containing
> gmxcheck_s -f md.trr

> # dump the last frame with higher precision
> trjconv -f md.trr -s b4md.tpr -n index.ndx -o frame.gro -ndec 6 -dump 
> 1234
> #  convert the dumped frame back to trr format
> trjconv -f frame.gro -n index.ndx -o frame.trr
> #  generate new tpr file with restart coordinates & velocities
> tpbconv -f frame.trr -s b4md.tpr -n index -e md_ener.edr -o restart.tpr
> #  Re-start with the new tpr file
> mdrun -s restart.tpr -o md2.trr ...
There is no need of all this. Just use the last one:
tpbconv -s traj.trr -s traj.tpr -o new.tpr
mdrun -s new.tpr -o ....

you can use the -until or -extent the trajectory if the run is finished. 
If it is not
finished the tpbconv will notice and generate a new.tpr to finish the 
initial run.


 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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