[gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory

[Tanping Li]

Dear Tsjerk,

Thanks for your help.

I run the two jobs on a cluster, maybe on different
nodes;

After just a few hundreds ps, the coordinates of the
system differs a lot. When I calculate the distance
between two atoms, there is about 1.5A difference;

Everything else in mdp file is exactly same.


Yours
Tanping


 

--- Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Tanping Li,
> 
> Can you be more elaborate? What are the differences?
> What do you mean with
> "totally different"? Did you run it on the same
> machine? Was everything else
> the same?
> 
> Cheers,
> 
> Tsjerk
> 
> On 10/5/07, Tanping Li <jia_11_osu at yahoo.com> wrote:
> >
> > Dear all,
> >
> > I run a 1ns trajectory for a protein in water. by
> > accidence, I find that the minor different in mdp
> file
> > gives two totally different trajectories. By
> setting
> >
> > nstxou=500
> > nstvou=500;
> >
> > and
> >
> > nstxou=2500
> > nstvou=2500;
> >
> > There is very large difference between two
> > trajectories (dt=2fs in both cases). I am really
> > confused: nstxou JUST sets the frequency to output
> the
> > coordinate, why I get different results? Looking
> > forward to your opinion and thanks a lot.
> >
> > Yours
> > Tanping Li
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> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
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