Fork me on GitHub

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/scripts directory and are based on the Groovy scripting langauge. 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

Optimization and Sampling

Minimization Algorithms, Simulated Annealing, MD, Alchemical Free Energy Simulations.

Potential Energy

Calculate Potential Energy, Test the Analytic Gradient, Time Energy and Gradient.

Real Space Refinement

Optimize an atomic resolution structure against real space data (i.e. CryoEM data).


Utilities to convert between file types or expand from a space group into P1.

X-ray Crystallography Refinement

Algorithms to optimize an atomic resolution structure against X-ray crystallography data.