Merge pull request #236 from jthorton/coords_fix

Fixes #235
leeping · Sep 17, 2021 · 0d63ac5 · 0d63ac5
2 parents 128d5bd + 64b9959
commit 0d63ac5
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/src/openmmio.py b/src/openmmio.py
@@ -1288,12 +1288,15 @@ def normal_modes(self, shot=0, optimize=True, for_hessian_target=False):
 
  def _update_positions(self, X1, disable_vsite):
  """A convenience method for updating the positions of the simulation context."""
+ # check if we have units
+ if isinstance(X1, numpy.ndarray):
+ X1 = X1 * angstrom
 
  if disable_vsite:
- self.simulation.context.setPositions(X1 * angstrom)
+ self.simulation.context.setPositions(X1)
  else:
  # Create virtual sites before setting positions
- mod = Modeller(self.pdb.topology, X1*angstrom)
+ mod = Modeller(self.pdb.topology, X1)
  mod.addExtraParticles(self.forcefield)
  self.simulation.context.setPositions(ResetVirtualSites_fast(mod.getPositions(), self.vsinfo))
 

diff --git a/src/smirnoffio.py b/src/smirnoffio.py
@@ -534,7 +534,7 @@ def _update_positions(self, X1, disable_vsite):
  else:
  X1 = (X1 + [Vec3(0.0, 0.0, 0.0)] * n_v_sites) * angstrom
 
- self.simulation.context.setPositions(X1 * angstrom)
+ self.simulation.context.setPositions(X1)
  self.simulation.context.computeVirtualSites()
 
  def interaction_energy(self, fraga, fragb):