BioSimSpace.Metadynamics

The Metadynamics package contains tools automatically configure, run, and analyse metadynamics simulations.

Metadynamics support requires PLUMED. We provide support for version 2.5 and above. Once installed, make sure that the plumed binary is visible in your PATH so that it can be found by BioSimSpace. You will also need to ensure that the PLUMED kernel is visible, and likely need to update your LD_LIBRARY_PATH too, e.g:

export PLUMED_KERNEL=/usr/local/lib/libplumedKernel.so
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

To use PLUMED you will also have to patch an appropriate molecular dynamics engine, following the instructions here. At present we only support metadynamics simulations using GROMACS.

Functions

run(system, protocol[, auto_start, name, …])

Auto-configure and run a metadynamics process.

Classes

Bound(value[, force_constant, exponent, epsilon])

Grid(minimum, maximum[, num_bins])