Unverified Commit f0bbea98 authored by Alex Izvorski's avatar Alex Izvorski Committed by GitHub
Browse files

Add OPC and OPC3 ion sets (#3819)

* copy opc ions and opc*standard.xml from https://github.com/openmm/openmmforcefields/commit/b12c2e871b60275a10b3f8f56dfc2f6d5447591f

* auto-merged files

* move charges to residue definition

* remove unmerged files

* add docs

* rename U to U4+

* rename Ag+, Tl+, Gd3+ and I- residue names

* fix O-H bond length typo

* add opc3 constraints test
parent 34446311
......@@ -505,6 +505,8 @@ File Parameters
:file:`amber14/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions
:file:`amber14/tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` and ions
:file:`amber14/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions
:code:`amber14/opc.xml` OPC water model\ :cite:`Izadi2014` and ions
:code:`amber14/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions
=================================== ============================================
As a convenience, the file :file:`amber14-all.xml` can be used as a shortcut to include
......
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......@@ -17,7 +17,7 @@
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="OW" class2="HW" length="0.978882" k="502416.0"/>
<Bond class1="OW" class2="HW" length="0.0978882" k="502416.0"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<!-- angle = arccos(1 - (1.598507**2 / (2*0.978882**2))) -->
......
......@@ -1325,6 +1325,13 @@ self.scriptExecuted = True
# -2532.4862082354407
self.assertTrue(abs(energy1 - energy_amber) < energy_tolerance)
context.applyConstraints(1e-12)
state = context.getState(getEnergy=True)
energy2 = state.getPotentialEnergy().value_in_unit(kilocalorie_per_mole)
self.assertTrue(abs(energy1 - energy_amber) < energy_tolerance)
self.assertTrue(abs(energy1 - energy2) < energy_tolerance)
class AmoebaTestForceField(unittest.TestCase):
"""Test the ForceField.createSystem() method with the AMOEBA forcefield."""
......
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