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 <[email protected]
<mailto:[email protected]>> 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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