[gmx-users] creation of edr files in mdrun

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 15 11:52:54 CET 2003

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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