[MMTK] solvation of protein molecule

Konrad Hinsen research at khinsen.fastmail.net
Fri Jun 4 08:05:20 UTC 2010


On 4 Jun 2010, at 03:25, prabhakar g wrote:

> I tried to solvate a protein molecule using the solvation.py, and am  
> getting two output files corresponding to solvation and  
> equilibration. When i try to visualize the file equilibration.nc  
> with the VMD, i am getting images of distorted water molecules  
> ( probably the bond lengths in them). I am attaching the image of  
> one of the distorted snapshot and the script for you reference, why  
> does this happen, is there anyway to correct it, hope somebody can  
> help. Thanks


VMD analyzes the first configuration of a trajectory to place bonds  
between atoms, based on distance criteria. It then keeps its list of  
bonded atom pairs unchanged for the rest of the trajectory. For a  
system with periodic boundary conditions, that is not a good method.  
Fortunately, it is sufficient to change the representation style to  
"dynamic bonds" for getting rid of this problem. The bonds are then  
recalculated for each frame.

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at  khinsen dot fastmail dot net
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