APBS Plugin: Settings Window

This window provides access to plugin-specific configuration options.

APBS Location and Working Directory

The full path to the APBS executable and Working Directory can be entered in these fields. The "Browse" button opens a file/directory selector to help find the path of either field.

The APBS configuration file and all necessary molecules (in PQR format) are written to the working directory before APBS is run. Any files created by APBS will also be located here, including maps. Note that the APBS plugin doesn't automatically delete any files created during the course of an APBS Run, so it may be necessary to manually empty the working directory periodically.

Miscellaneous Options

If the "Setup files only..." option is selected, the plugin will write an APBS configuration file and all necessary molecules to the working directory, without calling APBS to make any calculations. This allows the plugin to be used for more complicated APBS runs, in case an option is unavailable in the ELEC Window. It is also useful if APBS is to run on a different host than the one upon which VMD is running.

The plugin can be configured to override the atom radii currently loaded in VMD with those listed in a CHARMM parameter file. This is useful when VMD's simple radius-guessing heuristic is inappropriate for electrostatics calculations. Note that atom radii are only guessed by VMD when no radius information has been explicitly loaded by a file-format that supports it.