Software installation, dependencies, and logistics

The tutorials and software we provide rely heavily on the following software packages. The functions of each piece of software are described, so that researchers may make substitutions where appropriate.

Package Management

It is highly recommended to use a package manager to install the relevant code. Conda is recommended, and some packages are available only through pip (which comes with conda).

  1. conda
  2. pip

Molecular Dynamics

  1. OpenMM

    Particle simulations, used for both all-atom and coarse-grained simulations.

    conda install -c omnia openmm

  2. Packmol

    For packing and initializing large molecular systems.

  3. MDTraj

    For manipulating and analyzing molecular dynamics trajectories

    conda install -c conda-forge mdtraj

Coarse Graining

  1. Sim-Utils

    Interface and utilities for running and driving the coarse-graining package used at BioPACIFIC. While the interface for manipulating and working with system definitions and force fields is public, for access to the underlying coarse-graining engine, contact BioPACIFIC.

Field Theory

  1. PolyFTS

    In-house field theory package maintained by Professor Glenn Fredrickson's group. For access, contact BioPACIFIC.

  1. LAMMPS - particle based simulation
  2. cgOpenMM - coarse grained simulations built on top of the OpenMM engine
  3. HOOMD-blue - GPU accelerated coarse grained particle simulations
  4. Freud - analysis tools of self assembling systems
  5. VOTCA - another open source coarse graining package
  6. MoSDeF - a package of tools for setting up simulations.