OpenMM Nonbonded Slicing Plugin
This OpenMM plugin contains the SlicedNonbondedForce class, a variant of OpenMM's NonbondedForce. By partitioning all particles among $n$ disjoint subsets, the total potential energy becomes a linear combination of contributions from pairs of subsets like
E = \sum_{I=0}^{n-1} \sum_{J=I}^{n-1} \left( \lambda^{vdW}_{I,J}E^{vdW}_{I,J}+\lambda^{elec}_{I,J}E^{elec}_{I,J} \right)
where each slice is defined by subsets $I$ and $J$, superscripts vdW and elec denote van der Waals and electrostatic contributions, $E_{I,J}$ is the potential energy of all particle pairs formed by one particle in subset $I$ and one in subset $J$, and $\lambda_{I,J}$ is a scaling parameter.
By default, all scaling parameters are constant and equal to 1. However, the user can turn selected
scaling parameters into variables and store their values in Context global parameters. Derivatives
with respect to these variables can be requested and used, for instance, to report individual energy
slice contributions or sums thereof via getState with option getParameterDerivatives=True.
Documentation
Documentation for this plugin is available at Github Pages. It includes the Python API and the theory for slicing lattice-sum energy contributions.
Installation
The plugin is distributed on conda-forge:
mamba install -c conda-forge openmm-nonbonded-slicing
Instructions for building from source are in the documentation.
Usage
import openmm as mm
import nonbondedslicing as nbs
system = mm.System()
force = nbs.SlicedNonbondedForce(2)
system.addForce(force)
1 maintainer
Metadata
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Release files for openmm-nonbonded-slicing 0.3.0.post2
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Built distributions (wheels)
Total release size: 7.2 MB
Release files / openmm_nonbonded_slicing-0.3.0.post2-cp314-cp314-manylinux_2_34_x86_64.whl
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| Size | 858.9 kB |
| Tags | CPython 3.14 Linux glibc 2.34+ x86-64 |
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