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Fix #234 #235

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merged 5 commits into from
Oct 9, 2024
Merged

Fix #234 #235

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265bf81
Fix for repex in NPT ensemble
mb2055 Sep 26, 2024
2a0c15d
Changelog
mb2055 Sep 26, 2024
9982932
Replica exchange now has the correct signs
mb2055 Sep 30, 2024
d4f7e83
Multiply out -1 to simplify expression
mb2055 Oct 4, 2024
03b7b90
Fix sign in volume correction term. [ci skip]
lohedges Oct 4, 2024
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1 change: 1 addition & 0 deletions doc/source/changelog.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
* Add support for boresch restraints to PME.
* Port SOMD torsion fix to PME code.
* Fix issues with ``atomtype`` and ``atom`` records for dummy atoms in GROMACS topology files.
* Fixes issue with runnning ``sire.morph.replica_exchange`` on systems in an NPT ensemble.


`2024.2.0 <https://github.com/openbiosim/sire/compare/2024.1.0...2024.2.0>`__ - June 2024
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18 changes: 8 additions & 10 deletions src/sire/morph/_repex.py
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Expand Up @@ -87,13 +87,15 @@ def replica_exchange(
# delta = beta_b * [ H_b_i - H_b_j + P_b (V_b_i - V_b_j) ] +
# beta_a * [ H_a_i - H_a_j + P_a (V_a_i - V_a_j) ]

from ..units import k_boltz
from ..units import k_boltz, mole

N_A = 6.02214076e23 / mole

beta0 = 1.0 / (k_boltz * temperature0)
beta1 = 1.0 / (k_boltz * temperature1)

if not ensemble0.is_constant_pressure():
delta = beta1 * (nrgs1[0] - nrgs1[1]) + beta0 * (nrgs0[0] - nrgs0[1])
delta = beta1 * (nrgs1[1] - nrgs1[0]) + beta0 * (nrgs0[0] - nrgs0[1])
else:
volume0 = replica0.current_space().volume()
volume1 = replica1.current_space().volume()
Expand All @@ -102,8 +104,8 @@ def replica_exchange(
pressure1 = ensemble1.pressure()

delta = beta1 * (
nrgs1[0] - nrgs1[1] + pressure1 * (volume1 - volume0)
) + beta0 * (nrgs0[0] - nrgs0[1] + pressure0 * (volume0 - volume1))
(nrgs1[1] - nrgs1[0]) + (pressure1 * (volume1 - volume0) * N_A)
) + beta0 * ((nrgs0[0] - nrgs0[1]) + (pressure0 * (volume0 - volume1) * N_A))

from math import exp

Expand All @@ -118,12 +120,8 @@ def replica_exchange(
replica1.set_lambda(lam0)

if ensemble0 != ensemble1:
replica0.set_ensemble(
ensemble1, rescale_velocities=rescale_velocities
)
replica1.set_ensemble(
ensemble0, rescale_velocities=rescale_velocities
)
replica0.set_ensemble(ensemble1, rescale_velocities=rescale_velocities)
replica1.set_ensemble(ensemble0, rescale_velocities=rescale_velocities)

return (replica1, replica0, True)
else:
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