[gmx-users] restarting a run using tpbconv

N-J.M. Macaluso njmm2 at cam.ac.uk
Sat Jul 21 16:15:20 CEST 2007

This may be a trivial question, but how do you save velocities in this 
case? Would it be in the .mdp file or in the tpbconv command?

Thanks for your help,


On Jul 21 2007, David van der Spoel wrote:

>N-J.M. Macaluso wrote:
>> Hello,
>>    I am running a very long simulation, and the cluster I'm using has a 
>> wall time. I am using tpbconv to restart my simulations from a frame in 
>> the last run, but this doesn't seem to be working. When I analyze the 
>> second trajectory, the starting structure looks identical to the 
>> starting structure I had from the beginning. I am not sure if I am 
>> correctly using tpbconv.
>> I'm taking the completed trajectory of the run I want to continue and 
>> start the second run from the 1300 ps frame:
>> tpbconv -s protein.tpr -f protein.trr -o protein2.tpr -time -1300
>> Then I submit the continued job with this command:
>> mdrun -s protein2.tpr -o protein2.trr -c protein2.gro -g protein2.log -e 
>> protein2.edr -np 16
>> Like I said, it doesn't seem to start the second run from the specified 
>> frame, but rather runs the simulation from the starting structure. I 
>> would appreciate any help.
>you should save your velocities at regular intervals.  it will start 
>from that last save velocities (t=0 in your case).
>> Thanks,
>> Max Macaluso
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