[gmx-users] creation of edr files in mdrun

Sidney Elmer 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
> file).
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

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.


More information about the gromacs.org_gmx-users mailing list