psfgen_logfilefile nameclose Purpose: Open or close a log file to store all information printed to the console.
: 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.
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.
vpbonds1 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.