[MMTK] solvation of protein molecule

Konrad Hinsen research at khinsen.fastmail.net
Tue Jun 8 19:10:21 UTC 2010


On 8 Jun 2010, at 13:14, prabhakar g wrote:

> 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.

Certainly. You can have any box size and shape, and then put in  
whatever you like, so nothing prevents you from using the unit cell  
and the crystallographicallly observed molecules. However, for most  
protein crystals, this is likely to yield an unstable simulation  
because such a system is highly unrealistic. In a real crystal, the  
regions where crystallographers don't see molecules are not empty.  
They contain molecules that move too much to be seen. Replacing these  
molecules by vacuum is a rather drastic modification, which often  
leads to unstable simulations.

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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