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workaround for OpenMM's bug on nb force update parameters #13

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workaround for OpenMM's bug on nb force update parameters #13

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9 changes: 8 additions & 1 deletion grand/samplers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -404,6 +404,10 @@ def adjustSpecificWater(self, atoms, new_lambda):
# Get lambda values
lambda_vdw, lambda_ele = get_lambda_values(new_lambda)

state = self.context.getState(getPositions=True, enforcePeriodicBox=True, getEnergy=True)
positions = state.getPositions(asNumpy=True)
box_vectors = state.getPeriodicBoxVectors(asNumpy=True)

# Loop over parameters
for i, atom_idx in enumerate(atoms):
# Obtain original parameters
Expand All @@ -420,7 +424,10 @@ def adjustSpecificWater(self, atoms, new_lambda):
# Update context with new parameters
self.nonbonded_force.updateParametersInContext(self.context)
self.custom_nb_force.updateParametersInContext(self.context)


self.context.setPositions(positions)
self.context.setPeriodicBoxVectors(*box_vectors)

return None

def report(self, simulation):
Expand Down