4.9 Plugin for free-energy calculations with molecular dynamics: PLUMED

Molecular dynamics based free-energy calculations can be performed with the aid of the external plugin PLUMED.
Methods included are metadynamics [185], well-tempered metadynamics [22], umbrella sampling [299, 182, 265], Jarzynski-equation based steered molecular dynamics [156, 68]. A large and nearly exhaustive set of collective variable (CV) is accessible through a simple input script.

PLUMED is a free package that, after registration, can be downloaded from http://merlino.mi.infn.it/~plumed/PLUMED/Home.html Currently, a copy of the PLUMED library is kept in the external directory of the FHI-aims source code, and must be compiled separately using the makefile Makefile.meta (see section I.2). In the future a patch for modifying FHI-aims in order to compile it with PLUMED will be available on the PLUMED webpage.

4.9.1 Usage

The actual use of the plugin is switched on by this single line in control.in:

 plumed .true.

With plumed .false. (default) or nothing, the code would behave exactly as compiled without this plugin. It is implied that some MD scheme must be used in control.in, in order to see PLUMED acting. What PLUMED does, in facts, is to modify the molecular dynamics forces according to the selected scheme.
All the specific controls of the free energy calculation are contained in the file plumed.dat (which must be in the working directory, together with control.in and geometry.in, if plumed .true. is set). For all the details on plumed.dat, we defer to PLUMED manual which can be found on the project website.
Here we report a minimal example for metadynamics:

PRINT W_STRIDE 10
DISTANCE LIST 1 <g1> SIGMA 0.35
g1->
2 3 4
g1<-
HILLS HEIGHT 0.003 W_STRIDE 10
ENDMETA

This script would make PLUMED deposit Gaussians (HILLS) of HEIGHT $0.003$ hartree, every W_STRIDE timesteps. The (only) CV that will be biased by metadynamics is a distance between atom ‘1’ and the center of mass of atoms ‘2’, ‘3’, and ‘4’. The number labelling the atoms follows their order of appearance in geometry.in. The results will be printed (see below) every PRINT W_STRIDE time steps. The width of the Gaussian for the distance CV is specified by SIGMA

A note on the units: the units in plumed.dat and in the output(s) are the internal ones in FHI-aims, i.e. energies in hartree, distances in bohr, forces in hartree/bohr.

When using PLUMED, some extra output files are created. In log.dat the specifics of the run are given. COLVAR contains the trajectory of the selected CVs. Notably, if no biasing method is selected, but one or more CVs are defined in plumed.dat, PLUMED prints nonetheless the trajectory of those CVs in COLVAR (one can also explicitly switch off the biasing of some CVs via the NOHILLS directive).
In case metadynamics is used, then also HILLS is generated, which contains the informations for reconstructing the free energy profile. This is done with the postprocessing tool, “sum_hills”, which is given with the distribution.
For umbrella sampling a powerful tool for reconstructing the free-energy from COLVAR, can be downloaded from: http://membrane.urmc.rochester.edu/Software/WHAM/WHAM.html.