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:
- fileame.properties
- 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 |
---|---|
Specify the functional form of the force field, including bonded terms, van der Waals and electrostatics. |
|
Define PME electrostatics parameters such as real space cutoff, interpolation order and mesh density. |
|
Control details of structural refinement against experimental data sets and advanced force fields. |
|
Define the size of the simulation cell, spece group symmetry and use of PBC. |
|
Properties associated with the GK Implicit Solvent Model. |