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

Xavier Periole x.periole at rug.nl
Mon May 23 15:39:19 CEST 2005

Jian Zou wrote:

> Hi all,
> In the gmx-manual page for grompp, it says:
> "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 I want to continue a crashed run with tpbconv, need I set "gen_vel 
> = no" in the mdp file?
you do not need a mdp file when using tpbconv. The information is 
included in th tpr file
you give to tobconv. You need to change the gen_vel to no, only when you
strat from a gro file and mdp files.

> Another question is about how to restart a crashed run.
> Suppose the total no. of steps is 10000, dt=1fs, and the simulation 
> crashed at 5000 steps, T P coupling used, nstvout=1000, gen_vel=no,
> I tried
>> tpbconv -f md.trr -s b4md.tpr -n index.ndx -e md_ener.edr -o rerun.tpr
>> mdrun -s rerun.tpr ...
> but the restarted simulation seems to begin at the very beginning 
> (t=0, not t=5ps).
You migh have writen the trr file not often enought. So nothing has been 
writen before the crash.
If nothing has been written in it. tpbconv generate a tpr from the 


 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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