[gmx-users] Problem to save xtc file in single precision in 2 fs intervals

[Berk Hess]

> From: X.Periole at rug.nl
> Subject: Re: [gmx-users] Problem to save xtc file in single precision	in 2 fs	intervals
> To: gmx-users at gromacs.org
> Date: Wed, 18 Jun 2008 15:58:38 +0200
> 
> On Wed, 18 Jun 2008 10:54:56 -0300
>   Alberto Sergio Garay <sgaray at fbcb.unl.edu.ar> wrote:
> > Hi
> > 
> > 
> > I' ve been working in a particular problem which needs to save my 
> > trajectory in 2 fs intervals. The first 2ns of the trajectory was OK,  but 
> >after that gmxcheck showed me:
> > 
> > 
> > 2048.16 don't match (0.00219727, 0.00170898)
> > 
> > 2048.40 don't match (0.00219727, 0.00170898)
> > 
> > ...........................................................................
> > 
> > 
> > It looks as it is a precision problem. Doesn't it?
> 
> you may want to change the units of the trajectory. It is ps by default
> but can be changed to fs using trjconv.

Changing the units has no effect on the precision, it will only shift
the decimal point.

There is no real problem here, except that your times are not very accurate.
I think this has little or no effect on most things you want to do with it.

Berk.


> 
> > 
> > I used 1 fs for integration time, and the run did not show any other  error 
> >message.
> > 
> > Is there any way to correct this problem keeping the calculation in  single 
> >precision?
> > 
> > Thanks in advance.
> > -- 
> > 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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> 
> -----------------------------------------------------
> XAvier Periole - PhD
> 
> NMR & Molecular Dynamics Group
> University of Groningen
> The Netherlands
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------
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