External Program Forces

This feature allows an external program to be called to calculate forces at every force evaluation, taking all atom coordinates as input.

• extForces $<$ Apply external program forces? $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: Specifies whether or not external program forces are applied.

• extForcesCommand $<$ Force calculation command $>$
  Acceptable Values: UNIX shell command
  Description: This string is the argument to the system() function at every forces evaluation and should read coordinates from the file specified by extCoordFilename and write forces to the file specified by extForceFilename.

• extCoordFilename $<$ Temporary coordinate file $>$
  Acceptable Values: UNIX filename
  Description: Atom coordinates are written to this file, which should be read by the extForcesCommand. The format is one line of ``atomid charge x y z'' for every atom followed by three lines with the periodic cell basis vectors ``a.x a.y a.z'', ``b.x b.y b.z'', and ``c.x c.y c.z''. The atomid starts at 1 (not 0). For best performance the file should be in /tmp and not on a network-mounted filesystem.

• extForceFilename $<$ Temporary force file $>$
  Acceptable Values: UNIX filename
  Description: Atom forces are read from this file after extForcesCommand in run. The format is one line of ``atomid replace fx fy fz'' for every atom followed by the energy on a line by itself and then, optionally, three lines of the virial ``v.xx v.xy v.xz'', ``v.yx v.yy v.yz'', ``v.zx v.zy v.zz'' where, e.g., v.xy = - fx * y for a non-periodic force. The atomid starts at 1 (not 0) and all atoms must be present and in order. The energy is added to the MISC output field. The replace flag should be 1 if the external program force should replace the forces calculated by NAMD for that atom and 0 if the forces should be added. For best performance the file should be in /tmp and not on a network-mounted filesystem.