Configuration file modifications

The following configuration parameters are used to setup and run a Go simulation:

• GoForcesOn $<$ Are Go forces turned on? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not Go forces should be calculated. If turned `off', Go forces will not be calculated. If turned `on', Go forces will be calculated. By default, the Go forces will be calculated in addition to the electrostatic and van der Waals forces. To simulate a system using only Go forces, the partial charges and Lennard-Jones parameters can be set to zero in the force field files.

• GoParameters $<$ Parameter file defining Go potential $>$
  Acceptable Values: file
  Description: File contains parameters to define the Go pairwise forces between different chain types. All possible chain type pairing combinations must be enumerated. Chain types are defined in the GoCoordinates file. The format for the GoParameters file is described in the next section.

• GoCoordinates $<$ Reference structure for Go simulation $>$
  Acceptable Values: PDB file
  Description: PDB file contains the reference structure used to define the Go potential. The file need not be the same file used to initialize the coordinates of the MD simulation; however, it must contain the same number of atoms in the same order as given in the structure (.psf) and coordinates (.coor) file. Additionally, the occupancy fields of the PDB file will be read to determine which chain type an individual atom belongs to, and, thus, which pairwise Go potential to use to calculate forces. By default, the occupancy value of 0.0 turns off the Go potential for that particular atom.

• GoMethod $<$ controls method for storing Go contact information $>$
  Acceptable Values: lowmem or matrix
  Description: Specifies whether the Go contacts should be calculated on the fly or stored in a matrix respectively. In most cases, `lowmem' will be sufficient. However, for smaller systems, the `matrix' does offer a slight performance speedup in terms of wall time. Variable is only used if GoForcesOn is `on'

The following sections describe the format of the GoParameter file.