[MMTK] solvation of protein molecule

prabhakar g prabha.iisc at googlemail.com
Tue Jun 8 11:14:12 UTC 2010

Thank you Dr.Konrad Hinsen. I intend to do a molecular dynamics simulation
of a protein including only the crystallographic water molecules. Is it
possible to define a periodic boundary condition enclosing only the
crystallographic molecules using MMTK.


On Fri, Jun 4, 2010 at 5:05 PM, Konrad Hinsen <research at khinsen.fastmail.net
> wrote:

> 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.
> --
> ---------------------------------------------------------------------
> 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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