MoSDeF Cassandra

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Overview

MoSDeF Cassandra is a Python interface for the Cassandra Monte Carlo software. It offers complete integration with the MoSDeF tools and a user-friendly interface for Cassandra.

Warning

MoSDeF Cassandra is still in early development (0.x releases). The API may change unexpectedly.

Resources

  • Installation guide: Instructions for installing MoSDeF Cassandra

  • Key Concepts: How we think about MoSDeF Cassandra

  • GitHub repository: View the source code, contribute, and raise issues

  • Cassandra: Learn more about the Cassandra Monte Carlo software

  • Cassandra respository: View the source of the Cassandra Monte Carlo software

  • MoSDeF tools: A collection of tools for constructing systems and applying forcefield parameters for particle-based simulations

Citation

Please cite MoSDeF Cassandra, Cassandra, and the MoSDeF suite of tools if you use this tool in your research. See here for details.

Installation

Installation instructions are here. A conda installation is available:

conda create --name mc mosdef_cassandra -c conda-forge

Example

MoSDeF Cassandra provides a Python interface to Cassandra. The workflow consists of first constructing a system and move set. These two objects are passed to a function that calls Cassandra to perform the Monte Carlo simulation. The example below demonstrates an NVT Monte Carlo simulation of OPLS methane. No additional files are required. Everything required to run the Monte Carlo simulation is contained in the script below.

import mbuild
import foyer
import mosdef_cassandra as mc

# Create a methane molecule from a SMILES string
methane = mbuild.load("C", smiles=True)

# Load the forcefield via foyer
ff = foyer.forcefields.load_OPLSAA()

# Apply the forcefield parameters to methane with foyer
methane_ff = ff.apply(methane)

# Define an empty simulation box
box = mbuild.Box([3.0, 3.0, 3.0])

# Define the boxes, species in the system, molecules in the box
ensemble = 'nvt'
box_list = [box]
species_list = [methane_ff]
molecules_to_add = [[100]]

# Create the System
system = mc.System(box_list, species_list, mols_to_add=molecules_to_add)

# Create the MoveSet
moveset = mc.MoveSet(ensemble, species_list)

# Run a Monte Carlo simulation!
mc.run(
    system=system,
    moveset=moveset,
    run_type="equilibration",
    run_length=1000,
    temperature=300.0 * u.K
)

Several additional examples can be found here.

Credits

Development of MoSDeF Cassandra was supported by the National Science Foundation under grant NSF Grant Number 1835874. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

See here for complete credits.

Table of Contents

Getting Started

Guides

API

Reference

Indices and tables