[gmx-users] mdrun -rerun results depend on starting .gro file. Why?

[David Mobley]

Dear all,

I'm hoping someone can explain more thoroughly to me how exactly mdrun
-rerun works (Gromacs 3.2.1). Based on the manual, it looks like it should
be re-analyzing the trajectory I pass it. Thus, if I rerun the same
trajectory (with nstlist=1), I should get back the same energies, etc.

I've tried this several times on a particular system where I need to
reprocess some trajectories, and instead, the output depends on what
starting .gro file I use when I run grompp, not just on the .top and .trr
files that I use for mdrun -rerun. Exactly what role does the .gro file
play?

For example, if I reprocess a production trajectory after running grompp on
a .gro file that I used for equilibration, my reprocessed energies are
several percent different than they were when I first ran the trajectory. On
the other hand, if I reprocess the trajectory after running grompp with a
.gro file corresponding to the final frame of my original production
trajectory, I get exactly the same energies as I originally got.

So what role is the .gro file playing in the analysis? Why are my results
when I reprocess the trajectory dependent on the initial coordinates used
for grompp?

Thanks,
David Mobley
Dill group
UCSF
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