David,<br>
<br>
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.<br>
<br>
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. <br>
<br>
Or could you maybe check the source code for the -rerun option or something?<br>
<br>
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.<br>
<br>
Thanks,<br>
David<br>
<br>
<br><br><div><span class="gmail_quote">On 10/24/05, <b class="gmail_sendername">David</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Mon, 2005-10-24 at 14:43 -0700, David Mobley wrote:<br>> Dear all,<br>><br>> I'm hoping someone can explain more thoroughly to me how exactly mdrun<br>> -rerun works (Gromacs 3.2.1). Based on the manual, it looks like it
<br>> should be re-analyzing the trajectory I pass it. Thus, if I rerun the<br>> same trajectory (with nstlist=1), I should get back the same energies,<br>> etc.<br>><br>> I've tried this several times on a particular system where I need to
<br>> reprocess some trajectories, and instead, the output depends on what<br>> starting .gro file I use when I run grompp, not just on the .top<br>> and .trr files that I use for mdrun -rerun. Exactly what role does
<br>> the .gro file play?<br>><br>> For example, if I reprocess a production trajectory after running<br>> grompp on a .gro file that I used for equilibration, my reprocessed<br>> energies are several percent different than they were when I first ran
<br>> the trajectory. On the other hand, if I reprocess the trajectory after<br>> running grompp with a .gro file corresponding to the final frame of my<br>> original production trajectory, I get exactly the same energies as I
<br>> originally got.<br>><br>> So what role is the .gro file playing in the analysis? Why are my<br>> results when I reprocess the trajectory dependent on the initial<br>> coordinates used for grompp?<br><br>
It should not matter at all. The only difference in energies with the<br>original trajectory could be cause by chaning the tpr file. In principle<br>it is possible to give a completely different tpr file (e.g. for another
<br>protein) and do mdrun -rerun (as long as the number of atoms are the<br>same). Thus you have to take care that your new tpr file makes sense. I<br>suggest you try<br>gmxcheck -s1 old.tpr -s2 new.tpr | more<br>to inspect the differences.
<br><br><br><br>><br>> Thanks,<br>> David Mobley<br>> Dill group<br>> UCSF<br>> _______________________________________________<br>> gmx-users mailing list<br>> <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br>
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