[MMTK] restart from solvation example

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu Mar 15 07:33:48 UTC 2007


On 14.03.2007, at 22:18, Davide Ricci wrote:

> I've just finished to run the example of solvation of a small  
> molecule with water molecules. I've got the "equilibration.nc"  
> file, after a NPT run of 1000 steps. Now, I'd like to restart the  
> job, for a NVT runs, from the last configuration containing the  
> molecule+ the water environment. How I can do this ?

# Open the trajectory
trajectory = Trajectory(None, 'equilibration.nc')
universe = trajectory.universe

# Read the state from the last step
universe.setFromTrajectory(trajectory, -1)

# Remove the barostat
from MMTK.Environment import AndersenBarostat
barostat = universe.environmentObjectList(AndersenBarostat))
universe.removeObject(barostat)

# Go on with your simulation
...

Note that your trajectory does not contain velocities (assuming that  
you didn't modify the solvation script), so you have to re-initialize  
them and reequilibrate a bit.

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: hinsen at cnrs-orleans.fr
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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: hinsen at cnrs-orleans.fr
---------------------------------------------------------------------



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