[gmx-users] restarting a run using tpbconv

N-J.M. Macaluso njmm2 at cam.ac.uk
Sat Jul 21 15:52:52 CEST 2007


    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 

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.


Max Macaluso

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