[gmx-users] Minimum periodic distance

[Mark Abraham]

On 05/30/2011 03:36 PM, Kavyashree M wrote:
> 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 correct
> it now. or should I have to redo the simulation again??

We can't tell from the above description. Only you have the information 
about whether they really made such contact, and whether that's a 
serious problem. Make sure your observations above are not artefacts of 
periodicity.

Mark

> Kindly reply..
>
> Thank you
> With regards
> M. Kavyashree
>
> On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar <tsjerkw at gmail.com 
> <mailto: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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