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Fix issue #383 #384

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Merged
lohedges merged 3 commits into from
Nov 28, 2025
Merged

Fix issue #383 #384

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25e6c27
Use "0" for null EMLE interpolation force expression. [closes #383]
lohedges Nov 25, 2025
73005d2
Fix delta parameter in soft-core Coulomb term. [closes #385]
lohedges Nov 25, 2025
8fb9dc8
Fix delta parameter in ghost_14ff. [ci skip]
lohedges Nov 26, 2025
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4 changes: 4 additions & 0 deletions doc/source/changelog.rst
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Expand Up @@ -17,6 +17,10 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.

* Please add an item to this CHANGELOG for any new features or bug fixes when creating a PR.

* Use ``"0"`` for null EMLE interpolation force since ``""`` causes issues on some platforms.

* Fix ``delta`` parameter in soft-core Coulomb potential.

`2025.3.0 <https://github.com/openbiosim/sire/compare/2025.2.0...2025.3.0>`__ - November 2025
---------------------------------------------------------------------------------------------

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4 changes: 2 additions & 2 deletions doc/source/tutorial/part07/03_ghosts.rst
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Expand Up @@ -68,15 +68,15 @@ It is based on the following electrostatic and Lennard-Jones potentials:

.. math::

V_{\text{elec}}(r) = q_i q_j \left[ \frac{(1 - \alpha)^n}{\sqrt{r^2 + \delta_\text{coulomb}^2}} - \frac{\kappa}{r} \right]
V_{\text{elec}}(r) = q_i q_j \left[ \frac{(1 - \alpha)^n}{\sqrt{r^2 + \delta_\text{coulomb}}} - \frac{\kappa}{r} \right]

V_{\text{LJ}}(r) = 4\epsilon \left[ \frac{\sigma^{12}}{(\delta_\text{LJ} \sigma + r^2)^6} - \frac{\sigma^6}{(\delta_\text{LJ} \sigma + r^2)^3} \right]

where

.. math::

\delta_\text{coulomb} = \alpha \times \text{shift_coulomb}
\delta_\text{coulomb} = \alpha \times \text{shift_coulomb}^2

\delta_\text{LJ} = \alpha \times \text{shift_LJ}

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4 changes: 2 additions & 2 deletions src/sire/qm/_emle.py
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Expand Up @@ -45,7 +45,7 @@ def get_forces(self):

# Create a null CustomBondForce to add the EMLE interpolation
# parameter.
interpolation_force = _CustomBondForce("")
interpolation_force = _CustomBondForce("0")
interpolation_force.addGlobalParameter("lambda_emle", 1.0)

# Return the forces.
Expand Down Expand Up @@ -94,7 +94,7 @@ def get_forces(self):

# Create a null CustomBondForce to add the EMLE interpolation
# parameter.
interpolation_force = _CustomBondForce("")
interpolation_force = _CustomBondForce("0")
interpolation_force.addGlobalParameter("lambda_emle", 1.0)

# Return the forces.
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8 changes: 4 additions & 4 deletions wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp
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Expand Up @@ -1359,7 +1359,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system,
{
nb14_expression = QString(
"coul_nrg+lj_nrg;"
"coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha*alpha)+r_safe^2))-(kappa/r_safe));"
"coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha)+r_safe^2))-(kappa/r_safe));"
"lj_nrg=four_epsilon*sig6*(sig6-1);"
"sig6=(sigma^6)/(%3*sigma^6 + r_safe^6);"
"r_safe=max(r, 0.001);")
Expand All @@ -1372,7 +1372,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system,
{
nb14_expression = QString(
"coul_nrg+lj_nrg;"
"coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha*alpha)+r_safe^2))-(kappa/r_safe));"
"coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha)+r_safe^2))-(kappa/r_safe));"
"lj_nrg=four_epsilon*sig6*(sig6-1);"
"sig6=(sigma^6)/(((sigma*delta) + r_safe^2)^3);"
"r_safe=max(r, 0.001);"
Expand Down Expand Up @@ -1420,7 +1420,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system,
// kJ mol-1 given the units of charge (|e|) and distance (nm)
//
clj_expression = QString("coul_nrg+lj_nrg;"
"coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha*max_alpha)+r_safe^2))-(max_kappa/r_safe));"
"coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha)+r_safe^2))-(max_kappa/r_safe));"
"lj_nrg=two_sqrt_epsilon1*two_sqrt_epsilon2*sig6*(sig6-1);"
"sig6=(sigma^6)/(%3*sigma^6 + r_safe^6);"
"r_safe=max(r, 0.001);"
Expand Down Expand Up @@ -1458,7 +1458,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system,
// kJ mol-1 given the units of charge (|e|) and distance (nm)
//
clj_expression = QString("coul_nrg+lj_nrg;"
"coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha*max_alpha)+r_safe^2))-(max_kappa/r_safe));"
"coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha)+r_safe^2))-(max_kappa/r_safe));"
"lj_nrg=two_sqrt_epsilon1*two_sqrt_epsilon2*sig6*(sig6-1);"
"sig6=(sigma^6)/(((sigma*delta) + r_safe^2)^3);"
"delta=%3*max_alpha;"
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