Force Field X – Properties

Property Overview

Force Field X properties are defined using the following precedence order:

Highest precedence is given to the Java system properties mechanism:
- -Dkey=value from the Force Field X command line
- Equivalently, use the following code within a script before the structure file is opened.
```
System.setProperty("key","value")
```
Second highest precedence is given to structure specific properties. For example, when opening a structure named filename.pdb or filename.xyz, Force Field X will attempt to read properties from:
1. fileame.properties
2. filename.key (only if fileame.properties is not found)
User specific properties from the file ~/.ffx/ffx.properties.
Properties in the file defined by the environment variable FFX_PROPERTIES
Finally, properties are read in from force field definition files that are stored internally by Force Field X.

Property Groups

Force Field X properties are grouped into the following categories:

Property Group	Description
Electrostatics Functional Form	Provides a multiplicative scale factors that are applied to fixed partial charges, permanent atomic multipoles and induced dipoles.
Energy Unit Conversion	Set scale factors needed to convert the energy value computed by potential energy terms into units of kcal/mole. The correct values are force field dependent and typically provided in the header of the force field parameter file.
Implicit Solvent	Properties associated with the generalized Kirkwood implicit solvent model.
Local Geometry Functional Form	Set the value of the cubic, quartic, pentic and sextic terms in the Taylor series expansion form of bond, angle, Urey-Bradley and out-of-plane bend potential energy terms.
Non-Bonded Cutoff	Define how van der Waals, electrostatics and generalized Kirkwood interactions are cutoff.
Particle-Mesh Ewald Electrostatics	Define particle-mesh Ewald electrostatics parameters such as b-spline interpolation order and reciprocal space grid dimensions.
Potential Function Parameter	Specify potential energy function parameters for bonded terms, van der Waals interactions and electrostatics.
Potential Function Selection	Specify the functional form of the potential energy function, including bonded terms, van der Waals and electrostatics.
Unit Cell and Space Group	Define the simulation unit cell and space group symmetry.
Van Der Waals Functional Form	Define the functional form of van Der Waals interactions.
Structural Refinement	Control details of structural refinement against a target function defined by experimental data sets (X-ray, Neutron and/or CryoEM) and advanced force fields.