[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 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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