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Backport fix from PR #121 #122

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Merged
lohedges merged 1 commit into from
Feb 5, 2026
Merged

Backport fix from PR #121 #122

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16 changes: 16 additions & 0 deletions src/somd2/runner/_repex.py
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Original file line number Diff line number Diff line change
Expand Up @@ -309,6 +309,22 @@ def _create_dynamics(
):
from openmm.unit import angstrom

# Get the positions from the context.
positions = (
dynamics.context()
.getState(getPositions=True)
.getPositions(asNumpy=True)
) / angstrom

# The positions array also contains the ghost water atoms that
# were added during the GCMC setup. We need to make sure that
# we copy these over to the perturbed positions array.
diff = len(positions) - len(perturbed_positions)
if diff != 0:
perturbed_positions = _np.concatenate(
[perturbed_positions, positions[-diff:]]
)

dynamics.context().setPeriodicBoxVectors(*perturbed_box * angstrom)
dynamics.context().setPositions(perturbed_positions * angstrom)

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