[gmx-users] Minimum periodic distance

[Kavyashree M]

Hello sir,

I had used a dodecahedron cell for simulation. I have run
the simulation for 100ns, did you man I have to restart the
simulation again?

Thanking you
Kavya

On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Kavya,
>
> > "shortest periodic distance is 1.39714 (nm) at time 21824 (ps),
> > between atoms 2062 and 3688"
> > where 2062 is a protein atom and 21824 is a water molecule.
>
> 21824 is the time in ps at which the two atoms indicated, 2062 and
> 3688, are at the short distance given. You can dump the frame with
> trjconv and have a look. Probably your molecule stretched, or you
> solvated in a rectangular box and the protein rotated. In the first
> case, set a larger distance, in the second, use a rhombic
> dodecahedron.
>
> Cheers,
>
> Tsjerk
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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