[gmx-users] creation of edr files in mdrun
sidnasty at stanford.edu
Wed Jan 15 23:27:11 CET 2003
David van der Spoel wrote:
> On Wed, 2003-01-15 at 01:23, Sidney Elmer wrote:
> > I am using gromacs3.1.3. Is there a known bug or problem creating the
> > edr file with mdrun? The size of the file increases exponentially the
> > longer the simulation runs. And when I use g_energy, there are multiple
> > entries for a given time point. Initially, there is just one entry,
> > then it increass to three, then five, etc. For long runs, the size of
> > my edr file becomes exorbitantly large. Here is an example of the
> > output of g_energy. Specifically, notice that at 3260ps there starts to
> > be triplicate entries offset by +/- dt~0.002ps. Then, at 6520ps, five
> > entries are printed at offsets of dt ~0.002ps, again. At similar
> > increments (3260ps), the number of entries increases to seven, then
> > nine, then
> > eleven, etc. Before long, my file is huge due to all these duplicate
> > entries. Thanks.
> Is the edr file growing exponentially or the xvg?
> It seems like you have run g_energy -skip, then there is a check to see
> whether the (time MOD skip) = 0, but since it is floating point
> arithmetic there can be round off errors. If you don't use skip you
> should get output for each time you saved energy (nstenergy in mdp
> If it really is edr there is problem in mdrun (but there the arithmetic
> is done in integer)
> Groeten, David.
> Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576, 75123 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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It is the edr file that is growing exponentially. The energy.xvg being this
large is a consequence of multiple entries being saved in the edr file.
However, your email did shed light on what is happening. Mdrun isn't causing
the problems, but I realized after I sent the first email that the problem is
with eneconv. I am saving every time step from mdrun. Then, after the run
finishes, I use eneconv to "filter" the edr file using the -dt option (which
acts analogously to -skip). I think this will give some direction to find
out where the problem lies. Thank you.
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