New Commands in the version 2.0

• psfgen_logfile $<$ file name$>$ $[$ close$]$
  Purpose: Open or close a log file to store all information printed to the console.
  Arguments: $<$ file name$>$ : Valid file name in the current directory.
  close: Close the active log file. The file name should not be included in the closing command. Example above.
  Context: Any part of the script, context independent. May call multiple times.

• hmassrepart $[$ dowater $<$ 10$>$ $]$ $[$ mass $<$ target hydrogen mass$>$ $]$
  Purpose: Partition the mass of heavy atoms into the bonded hydrogen atoms.
  Arguments: dowater: 1 for true, 0 for false. Partition the water molecules. Default value 0.
  mass: Target for the hydrogen atoms' mass. Default value 3.024 amu.
  Context: After loading or preparing the structure.

• vpbonds $[$ 1 0$]$
  Purpose: Print the bonds between the virtual particles (drude particles and lone pairs) and their hosts.
  Arguments: 1 for true, 0 for false. Default value 1.
  Context: Before writing the psf file. May call multiple times. WARNING: To run simulations containing lone pairs or Drude particles on NAMD 2.13, set vpbonds to 0.