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

Jian Zou zouj01 at mails.tsinghua.edu.cn
Mon May 23 15:34:26 CEST 2005

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?

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 

Did I forget or misuse some options?

Thank you very much in advance.


Jian Zou

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