[gmx-users] Simulation in parts

toma0052 toma0052 at umn.edu
Wed Feb 21 21:38:18 CET 2007

     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.  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?  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?

Mike Tomasini

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