Pair interaction calculations

NAMD supportes the calculation of interaction energy calculations between two groups of atoms. When enabled, pair interaction information will be calculated and printed in the standard output file on its own line at the same frequency as energy output. The format of the line is PAIR INTERACTION: STEP: step VDW_FORCE: fx fy fz ELECT_FORCE: fx fy fz. The displayed force is the force on atoms in group 1 and is units of kcal/mol/Å.

For trajectory analysis the recommended way to use this set of options is to use the NAMD Tcl scripting interface as described in Sec. 2.2.2 to run for 0 steps, so that NAMD prints the energy without performing any dynamics.

• pairInteraction $<$ is pair interaction calculation active? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether pair interaction calculation is active.

• pairInteractionFile $<$ PDB file containing pair interaction flags $>$
  Acceptable Values: UNIX filename
  Default Value: coordinates
  Description: PDB file to specify atoms to use for pair interaction calculations. If this parameter is not specified, then the PDB file containing initial coordinates specified by coordinates is used.

• pairInteractionCol $<$ column of PDB file containing pair interaction flags $>$
  Acceptable Values: X, Y, Z, O, or B
  Default Value: B
  Description: Column of the PDB file to specify which atoms to use for pair interaction calculations. This parameter may specify any of the floating point fields of the PDB file, either X, Y, Z, occupancy, or beta-coupling (temperature-coupling).

• pairInteractionSelf $<$ compute within-group interactions instead of bewteen groups $>$
  Acceptable Values: on or off
  Default Value: off
  Description: When active, NAMD will compute bonded and nonbonded interactions only for atoms within group 1.

• pairInteractionGroup1 $<$ Flag to indicate atoms in group 1? $>$
  Acceptable Values: integer
  Description:

• pairInteractionGroup2 $<$ Flag to indicate atoms in group 2? $>$
  Acceptable Values: integer
  Description: These options are used to indicate which atoms belong to each interaction group. Atoms with a value in the column specified by pairInteractionCol equal to pairInteractionGroup1 will be assigned to group 1; likewise for group 2.