The velocity is in the trr file. How many frames you have in
protein.trr? What's its last frame?
You also need to supply the energy file to tpbconv.
On 7/21/2007 10:15 PM, N-J.M. Macaluso wrote:
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,
Max
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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