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Property Overview

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

  1. 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")
  2. 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)
  3. User specific properties from the file ~/.ffx/ffx.properties.
  4. Properties in the file defined by the environment variable FFX_PROPERTIES
  5. 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

Force Field

Specify the functional form of the force field, including bonded terms, van der Waals and electrostatics.

Particle Mesh Ewald Electrostatics

Define PME electrostatics parameters such as real space cutoff, interpolation order and mesh density.

X-ray, Neutron and Real Space Refinement

Control details of structural refinement against experimental data sets and advanced force fields.

Unit Cell, Space Group and Periodic Boundary Conditions

Define the size of the simulation cell, spece group symmetry and use of PBC.

Implicit Solvent

Properties associated with the GK Implicit Solvent Model.