Force Field X – Commands

Command Overview

Force Field X commands are launched using the following syntax:

ffxc [-D<property=value>] <command> [-options] <PDB|XYZ>

Force Field X supports a variety of internal commands that are listed below. Information on the options available for a command is output if the help flag is specified following the command.

ffxc <command> -h

Custom modifications to a command, or the creation of a completely new command, is possible by launching Force Field X with a script file.

ffxc [-D<property=value>] <path/to/script.groovy> [-options] <PDB|XYZ>

Example scripts are located in the ffx/groovy directory and are based on the Groovy scripting language. Force Field X packages can be imported and used by following the FFX API documentation.

Available Commands

Available Force Field X commands are grouped into the following catagories:

Command Category	Purpose
Energy and Structure Analysis	Calculate Potential Energy, Test the Analytic Gradient, Time Energy and Gradient.
Optimization and Sampling	Minimization Algorithms, Simulated Annealing, MD, Alchemical Free Energy Simulations.
Real-Space Refinement	Optimize an atomic resolution structure against real space data (i.e. CryoEM data).
X-ray and Neutron Crystallography Refinement	Algorithms to optimize an atomic resolution structure against X-ray crystallography data.
Utilities	Utilities to convert between file types or expand from a space group into P1.