[MMTK] MD with fixed atoms

Konrad Hinsen research at khinsen.fastmail.net
Thu Apr 14 06:22:51 UTC 2011

On 14 Apr 2011, at 00:32, Victor Muñoz wrote:

> I'm trying to run a MD with MMTK. I want to define some atoms as  
> fixed, and as I have readed in the users manual, I'm giving them the  
> attribute fixed with value one, setting the rest of atoms as fixed =  
> 0. The way I'm doing it is the following:
> for a in self.universe.atomList():
>           if a in selected_atoms:
>                       a.fixed = 1
>           else:
>                       a.fixed = 0

That looks fine.

> were the selected_atoms are the atoms I want to maintain fixed. If i  
> print the atom.fixed value for every atom, I can see that the  
> previous code worked fine, and values 0 and 1 are given to  
> atom.fixed attribute. But when I run the simulation, none of the  
> atoms is kept as fixed. Maybe I am doing something wrong?

Can you post a simple example, ideally for a small system?

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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