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

David spoel at xray.bmc.uu.se
Tue Oct 25 00:11:40 CEST 2005

On Mon, 2005-10-24 at 14:43 -0700, David Mobley wrote:
> 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? 

It should not matter at all. The only difference in energies with the
original trajectory could be cause by chaning the tpr file. In principle
it is possible to give a completely different tpr file (e.g. for another
protein) and do mdrun -rerun (as long as the number of atoms are the
same). Thus you have to take care that your new tpr file makes sense. I
suggest you try
gmxcheck -s1 old.tpr -s2 new.tpr | more
to inspect the differences.

> Thanks,
> David Mobley
> Dill group
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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