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 (v0.4.3)

• Added time dependent umbrella centers (steered MD)
• Fixed biases resizing bug in ABF method

Features

SSAGES currently works with LAMMPS and Gromacs molecular dynamics engine. 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!

CVs

• Particle coordinate
• Particle position
• Particle separation
• Bend angle
• Torsional angle
• Radius of gyration

Methods

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

Installation

The first step is to clone the repository locally.

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

SSAGES uses a CMake build system. It also requires either the LAMMPS or Gromacs source codes. To compile, 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 ..

###Boost and MPI

SSAGES uses Boost MPI to provide a convenient MPI programming interface. The requirement is for Boost >= 1.58 with the MPI and serialization modules. A requisite underlying MPI library is also required. On recent Debian based systems using OpenMPI, the requirement can be installed via:

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

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 (v0.4.2)

• String method fix for compiling

What's Old (v0.4.1)

• String method fix for Gromacs

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.

• Restart capabilities are currently unimplemented in Gromacs

Contributing

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