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README.md

SSAGES

SSAGES (Software Suite for Advanced Generalized Ensemble Simulations) is an open-source, engine agnostic, C++11 based advanced sampling package. It is designed to be easy to use, extendable and extremely versatile. It is currently pre-beta, meaning that there are many rough edges, but we are working rapidly to expand its features and fix any bugs. Keep an eye on this page for future updates and see below on how to contribute!

What's New (v0.8.2)

  • Grid internal updates
  • ABF Integrator handles interpolation in each direction independently
  • ABF restarts now handled with JSON member
  • GyrationTensorCV can be projected into any number of dimensions
  • Documentation updates
  • Several bugfixes (See commits)

Features

SSAGES currently works with multiple molecular dynamics engines. It contains a variety of collective variables (CVs) and advanced sampling methods.

Highlights

  • Engine agnostic framework
  • Simple JSON input file syntax
  • Easy to add new CVs
  • Easy to add new methods
  • Much more!

Engines

  • GROMACS 5.1.x, 2016.x, 2018.x
  • LAMMPS (Most recent versions)
  • OpenMD (2.4+)
  • QBox (1.63+)

CVs

  • Atom group coordinate
  • Atom group position
  • Atom group separation
  • Bend angle
  • Box volume
  • Components of gyration tensor
  • Pairwise kernel (coordination number, nearest neighbors)
  • Polymer Rouse modes
  • Secondary structure (alpha, anti/parallel beta sheet) RMSD
  • Torsional angle

Methods

  • Adaptive biasing force
  • Artificial neural network sampling
  • Basis function sampling
  • Metadynamics
  • Umbrella sampling
  • Finite temperature string
  • Nudged elastic band
  • Swarm of trajectories
  • Forward flux sampling

Installation

The first step is to clone the repository locally.

$ git clone https://github.com/MICCoM/SSAGES-public.git

SSAGES uses a CMake build system. It also requires the use of a support MD engine. For example, to compile with LAMMPS, execute the following

$ cd SSAGES
$ mkdir build && cd build
$ cmake -DLAMMPS_SRC=/path/to/lammps/src .. 
$ make

This will build a SSAGES executable which will reside in the build directory.

If you want to compile and run unit and integration tests, replace the cmake command in the example above with

$ cmake -DLAMMPS_SRC=/path/to/lammps/src -DBUILD_TESTS=ON ..

MPI

A requisite underlying MPI library also required to run SSAGES. On recent Debian based systems using OpenMPI, the requirement can be installed via:

$ sudo apt-get install libopenmpi-dev openmpi-bin

For more detail on the build system, please check the documentation.

Build the documentation

After you have built SSAGES you can further build the documentation from the build/ directory. Make sure you have the following tools available:

  • doxygen
  • dot (part of the graphViz package)
  • sphinx (python-sphinx or python3-sphinx)
  • ReadTheDocs theme (pip install sphinx_rtd_theme)

You can build the documentation with

$ make doc

You can alse build the API-references and the User Manual separately with

$ make apiref

and

$ make manual

If you have pdflatex installed, you can also build a PDF file for the documentation. To compile the API-reference into a PDF file do

$ cd doc/API-doc/latex/
$ make

The pdf is called refman.pdf

Similarly, you can build a PDF version of the Manual with

$ cd doc/Manual/
$ make

The pdf-file will be called SSAGES.pdf

View the documentation

Once you have built the documentation you will find it in the doc/API-doc/ and doc/Manual directories. To view the documentation in a browser call for example

$ firefox doc/API-doc/html/index.html

or

$ firefox doc/Manual/index.html

What's Old (v0.8.1)

  • GROMACS support for all 5.1.x, 2016.x, 2018.x!
  • Better CMake handling for Hooks
  • Handling of LAMMPS line continuations (&)
  • Correct handling of multiprocessor ABF method
  • BFS method cleanup
  • Minor documentation updates
  • Eigen include update (3.3.4)
  • googletest include update (1.8.0)
  • jsoncpp include update

What's Old (v0.8.0)

  • Added ANN sampling!
  • More documentation updates
  • Updates to examples
  • Added Fourier and Chebyshev basis sets to BFS
  • Added 3D ABF integrator
  • Improved periodicity handling on grid
  • Secondary structure CV bug fixes
  • Improved Qbox integration

What's Old (v0.7.5)

  • Major documentation update!
  • Major examples update!
  • New generalized pairwise CV
  • New secondary structure CVs (alpha and anti/parallel beta sheet RMSD)
  • New CV logging capability
  • CV selection by name in methods
  • Updated unit tests
  • Updated ABF integrators for periodic and non-periodic CVs
  • Gromacs 2016.3 support!
  • Many bug fixes!

What's Old (v0.7.0)

  • New simplified JSON syntax
  • Support for multiple simultaneous methods!
  • Eliminated boost dependency!
  • CV selector for methods
  • Argument forwarding for Gromacs
  • Updated forward flux examples
  • Significant under-the-hood improvements
  • Fixed Gromacs auto-download

What's Old (v0.6.0)

  • Support for QBox first-principles MD engine
  • Support for OpenMD engine
  • Coordination number CV
  • Polymer Rouse modes CV
  • Box volume CV
  • Virial contribution (NPT support) for some CVs and methods
  • Updated examples and documentation
  • New backend grid
  • Grid-based metadynamics
  • Updated forward flux sampling
  • Fixed regression with string methods
  • Performance and other improvements!

What's Old (v0.5.0)

  • Gromacs restart support
  • New gyration tensor CVs
  • Updated examples and documentation
  • Metadynamics optimizations
  • Better engine error handling
  • More! (See commit log)

Known issues

SSAGES is currently in pre-beta. That means there may be known issues that are not yet resolved. Major issues are listed here.

  • Restarts are not fully functioning for all methods.

Contributing

Feel free to fork this project on GitHub. Any pull-requests, feature requests or other form of contributions are welcome.