Hi toma0052.
toma0052 wrote:
Hello,
I was wondering if I could run a simulation in parts. I would like to
run a simulation for 100ps say, analyze it, and then sometime later continue
on for another 100ps.
You can. When you restart you simulation make sure you use a grompp.mdp
file that does not generate velocities. "gen-vel =
no", "gen-temp = 300". You can run into problems however
if you trajectories from the first run are not complete, but thats
another story.
It seems like all I would need to do is take the
*.gro, *.trr, and *.edr files output from the first md simulation, feed it
back in to grompp and use mdrun. I have tried this, and the output from the
run seems okay, but I am not completely sure. The output of grompp says;
Velocities generated: ignoring velocities from input trajectory. Will this
cause a disjoint between the two simulations? Is there a way that I can have
the velocities from the end of the first md simulation, input into the
second?
If you ad the two ener.edr files together using enerconv (i think) you
can see if your second simulation is a continuation of the first.
Also, I used -time 100 and grompp says; Reading frame 500 time
100.000 Using frame at t = 100 ps
Starting time for run is 0 ps
Is there a way that I can have the starting time for the second run be 100ps
so that the numbers match up in the *.edr files and the second run goes from
100ps to 200ps?
If you run the two simulations separately you can ad the traj.trr and
the ener.edr files together afterwards. If the time is not sat right you
can do that manually using some some flagg.
Good luck.
/Calle
Thanks,
Mike Tomasini
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