[gmx-users] Rte: I can't understand gmxcheck output "don't match ..."

[Berk Hess]

Hi,

I think there is no problem at all.
The step 0.002 ps is so small that it can no longer accurate be stored
in a single precision time variable.
So there is nothing to worry about.

For this reason we should convert the time variables in Gromacs 
trajectories to double precision, but that would make all current
formats incompatible.

Berk.


> Date: Wed, 4 Jun 2008 07:58:11 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Rte: I can't understand gmxcheck output "don't match	..."
> 
> 
> The output is telling you that gmxcheck is finding an interval that does not
> match what it is expecting.  Did you assemble this trajectory from other
> pieces, and if so, how?  You might also find this thread informative, there are
> several suggestions there as to how such things occur:
> 
> http://www.gromacs.org/pipermail/gmx-users/2008-May/033814.html
> 
> -Justin
> 
> Quoting Alberto Sergio Garay <sgaray at fbcb.unl.edu.ar>:
> 
> > Hi
> >
> > I was checking a xtc file with gmxcheck (without any option) and I
> > obtained some
> > information which I could not understand:
> >
> > Reading frame 80 time 2100.160
> > Timestep at t=2100.16 don't match (0.00219727, 0.00170898)
> > reading frame 200 time 2100.400
> > Timestep at t=2100.4 don't match (0.00219727, 0.00170898)
> > reading frame 300 time 2100.600
> > Timestep at t=2100.64 don't match (0.00219727, 0.00170898)
> > ..........................................................
> >
> > What does these pairs of number mean at the end of each row (between
> > parenthesis)?
> >
> > Can I fix this problem?
> >
> > Any suggestion would be appreciated.
> >
> > --
> > Dr. Sergio Garay
> > Facultad de Bioquimica y Cs. Biológicas
> > Universidad Nacional del Litoral
> > Santa Fe - Argentina
> > C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
> > Argentina
> > Ph. +54 (342) 4575-213
> > Fax. +54 (342) 4575-221
> >
> >
> >
> >
> >
> > _______________________________________________
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> 
> 
> 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> 
> ========================================
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