OpenMM helper

This module provides various tools to simplify the usage or extend the functionality of OpenMM. Mainly, they can be categorized into file parsers, pre-constructed forces and reporters.

Forces

slab_correction(system)	Apply Yeh's long range coulomb correction for slab geometry in z direction to eliminate the undesired interactions between periodic slabs.
restrain_particle_number(system, particles, ...)	Restrain the number of selected particles in a region.
wall_lj126(system, particles, direction, ...)	Add a LJ-12-6 wall for selected particles so that they cannot cross it.
wall_power(system, particles, direction, ...)	Add a power wall for selected particles so that they cannot cross it.
point_wall_power(system, particles, ...[, power])	Add a spherical wall centered at a reference point so that selected particles are repelled from this point.
electric_field(system, particles, strength)	Apply external electric field to selected particles in a system.
spring_self(system, positions, particles, ...)	Restrain the selected particles at their original positions.
CLPolCoulTT(system, donors[, b])	Apply Tang-Toennies damping for the Coulomb interactions between selected H-bond donors and Drude dipoles.

Reporters

ViscosityReporter(file, reportInterval[, append])	ViscosityReporter report the velocity amplitude and reciprocal of viscosity using cosine periodic perturbation method.
DrudeTemperatureReporter(file, reportInterval)	DrudeTemperatureReporter reports the temperatures of different DOFs in a Drude simulation system.
GroReporter(file, reportInterval[, ...])	GroReporter outputs a series of frames from a Simulation to a GRO file.
CheckpointReporter(file, reportInterval[, xml])	CheckpointReporter saves periodic checkpoints of a simulation.
StateDataReporter(file, reportInterval[, ...])	StateDataReporter outputs information about a simulation, such as energy and temperature, to a file.

Parsers

GroFile(file)

GroFile is a parser and writer for Gromacs .gro file.