The parameters directory contains files specifying parameters for various aspects of the molecular dynamics simulations.
These files are used by the scripts to generate the inputs for the Plumed-patched Gromacs simulations.
mdp contains the molecular dynamics parameters (MDP) for Gromacs.
File specifications are described in the Gromacs manual.
The file names are important, as they are used by the scripts to call gmx grompp on the mdp files to generate the input tpr files for the simulations.
The files are placed in subdirectories according to the type of simulation they are used for.
The files in umbrella-sampling are more generally useful for simulations where 2 polymer chains are desired to be restrained at a specific distance from each other.
plumed contains the input files for the Plumed patch inside gmx mdrun.
These files should be called during a simulation with the -plumed flag.
We currently have template input files for simple harmonic restraints, OPES-Explore, HREMD, and OneOPES.