[gmx-users] mdrun -rerun results depend on starting .gro file. Why?
dmobley at gmail.com
Tue Oct 25 00:35:11 CEST 2005
That's what I thought, but the fact is, it IS making a significant
difference (several percent). I generate EXACTLY the same tpr file, with the
exception of the .gro file and nstlim=1, and I get different energies by
several percent. If I use the same .gro file I get the same energies. So
clearly there is some interplay going on. I've tried this multiple different
times on a number of different systems (in 3.2.1) and the effect is quite
reproducible. I am NOT doing something drastic like running it on a
different system or anything -- I'm running the SAME system, with everything
set the same, except nstlim=1, and a different .gro file for grompp.
Could you perhaps try the same experiment on your own system? Just try mdrun
-rerun of a trajectory by taking your original mdp file, setting nstlim=1,
and then generating a tpr file with your original system's starting
coordinates and processing your original trajectory with that tpr file and
-rerun. Then take your original system's ending coordinates (in my case,
I've got a protein which I'm running for 1 ns) and repeat the same process.
Compare the energies written out by the two and see if they're different;
I'm getting, as I said, differences of several percent.
Or could you maybe check the source code for the -rerun option or something?
I can even send you the system I'm working on if you want. I'm actually
running a very simple system with just toluene in water and I'm seeing this
difference; it's rather concerning, plus it's making it so I can't do the
data analysis I need.
On 10/24/05, David <spoel at xray.bmc.uu.se> wrote:
> 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
> > UCSF
> > _______________________________________________
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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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