[gmx-users] Minimum periodic distance

[Tsjerk Wassenaar]

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