CPPM generator

Overview

This is a single command-line tool that generates spherical Charged Patchy Particle Models (CPPM) which mimic bio-colloidal particles, e.g. globular proteins. The figure below shows examples of interacting CPPMs taken from https://doi.org/10.1063/1.4928077:

cppm-generator generates CPPMs by placing neutral, positive, and negative particles on the surface of a sphere, and minimise the (free) energy using Metropolis-Hastings Monte Carlo sampling.

Installing

$ cargo install cppm-generator

Usage

The default parameters produce an isotropic, charged particle similar to P00 from Table 1 in this publication. It is also possible to impose a target molecular dipole moment using the --dipole option.

$ cppm-generator --help
USAGE:
cppm-generator [OPTIONS] --file <FILE>
OPTIONS:
-b, --bjerrum-length <BJERRUM_LENGTH> Bjerrum length (Å) [default: 7.0]
-h, --help Print help information
-m, --minus <NUM_MINUS> Number of negative (-1e) particles [default: 37]
-N <NUM_TOTAL> Total number of particles [default: 643]
-o, --file <FILE> Output structure (.xyz or .pqr)
-p, --plus <NUM_PLUS> Number of positive (+1e) particles [default: 29]
-r, --radius <RADIUS> Sphere radius (Å) [default: 20.0]
-s, --steps <STEPS> Number of Monte Carlo iterations [default: 10000]
-u, --dipole <TARGET_DIPOLE_MOMENT> Target dipole moment (Debye)
-V, --version Print version information

Details and status

• Random walk on a sphere using spherical coordinates
• Particle-particle interactions using a Coulomb/softcore potential
• Arbitrary mixing of neutral and charged particles
• Output to .xyz and .pqr files
• Command line interface
• Dipole moment analysis
• External electric field to induce arbitrary patches
• Constrain to target dipole moment w. harmonic potential
• Written in Rust
• Use uon for dimensional analysis
• IO error handling
• Unittests
• Logging support

Motivation

Besides some scientific use, this project is mainly a first dive into the Rust programming language.