[gmx-users] weird nst*out problem

[Bert de Groot]

"K.A. Feenstra" wrote:
> 
> Bert de Groot wrote:
> > Hi all,
> >
> > we have noticed the weird problem that when the simulation time gets large
> > compared to nstxout, nstxtcout, or any of the other nst*out parameters,
> > then the output frequency in the .xtc, or .trr file becomes inaccurate.
> 
> I would think that not the output frequency is inaccurate, but the
> calculation that gmxcheck makes. gmxcheck subtracts frame times
> in single precision, which is about 6-7 digits. That will go wrong
> with times like 300000.312.
> 
> Output frequencies, as mdrun determines, are done using step number,
> which should be absolutely reliable, since that is all integer work.
> 

but, in that case, the times in the trajectory should be ok, right?
However, this is not the case (output from a tool that simply reads
the times from a .xtc file, which is btw also what tools like g_rms
etc report as times in the .xvg files for example):

   300000.00000
   300000.09375
   300000.18750
   300000.31250
   300000.40625
   300000.50000

which should have been:

   300000.00000
   300000.10000
   300000.20000
   300000.30000
   300000.40000
   300000.50000


Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________