[gmx-users] restarting a run using tpbconv

David van der Spoel spoel at xray.bmc.uu.se
Sat Jul 21 16:01:06 CEST 2007

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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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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