[MMTK] MD with fixed atoms

Victor Muñoz chewaka.87 at gmail.com
Wed Apr 13 22:32:03 UTC 2011


Dear all,

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

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?

Thanks for the help.

Kind regards,

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