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