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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