[gmx-users] Minimum periodic distance

Kavyashree M hmkvsri at gmail.com
Mon May 30 07:36:36 CEST 2011

Hello Sir,

I saw the 21824th frame, it dint look unusually stretched when
I superposed against the initial pdb file. there atoms were hydrogen
atoms of two lysine residues.. And in the entire strttch of 100ns simulation

this is the only periodic image interaction observed, Is it possible to
it now. or should I have to redo the simulation again??
Kindly reply..

Thank you
With regards
M. Kavyashree

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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