Hi This question is about trying to make sure that I am doing the right thing while trying to use tpbconv to restart jobs.
After minimization, for the first dynamics run, I use gen_vel = yes. For subsequent restart runs however, gen_vel must be set to no. After the first dynamics run of 200ps, my output is mol-1.edr/trr, and the input for the first dynamics run was mol-1.tpr I can then try to extend the simulation beyond 200 ps using tpbconv with the following options: tpbconv -f mol-1.trr -s mol-1.tpr -e mol-1.edr -extend 200 -o mol-2.tpr The problem with this, however, is that mol-1.tpr was built with gen_vel = yes, which should not be the case when one is restarting the simulation. First question: will this matter at all, because the velocities should be read from the .trr file anyway, and that should overwrite the information in the tpr file ? In order to circumvent the problem, and avoid deshuffling and reshuffling, I wrote another .tpr file for the first dynamics run but with gen_vel set to no. I did not use this tpr file to run the simulation. Lets call this tpr file mol-novelocity-1.tpr. So, the only difference between mol-1.tpr and mol-novelocity-1.tpr is that the former has initialized velocities, while the latter does not. Now, I can use tpbconv to restart the simulation as follows: tpbconv -s mol-1.tpr -f mol-1.trr -e mol-1.edr -extend 200 -o mol-2.tpr I just wanted to confirm if what I am doing makes sense ? Thanks very much for the help ! -Himanshu
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