[gmx-users] Minimum periodic distance
Mark.Abraham at anu.edu.au
Mon May 30 08:37:07 CEST 2011
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
> 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
> 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
> 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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