[gmx-users] Why did it start from the very beginning???

[Mark Abraham]

liu xin wrote:
> Hi GMX users
> 
> My 2ns simulation crashed accidentally, gmxcheck said my previous 
> simulation was stopped at 1400 ps, then I used the tpbconv to generate a 
> new tpr to restart it from the previous ending point:
> "tpbconv -f -e -s -o new.tpr"
> but I found the output message of tpbconv said:
> "1000000 steps (2000 ps) remaining from first run.
> Writing statusfile with starting step          0 and length    1000000 
> steps...
>                                  time      0.000 and length   2000.000 ps"
> and if I use the new.tpr, the simulation will run another 2ns! I doubt 
> that this new.tpr will restart my simulation from the beginning. Then I 
> tried -time 1300, -time 1000, -until 2000, the output message was the same.
> Did I use the tpbconv in a wrong way?

You need a trajectory frame with both positions and velocities... (and 
an energy frame from its file if you want an exact continuation of 
pressure-coupling or N-H T-coupling) I guess that only your first frame 
satisfies this. Consult the n???out flags in your original mdp file for 
the frequency with which you are writing velocities.

Mark