[gmx-users] Simulation in parts

Carl Caleman calle at xray.bmc.uu.se
Thu Feb 22 00:19:45 CET 2007

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.


> Thanks,
> Mike Tomasini
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