Section MOLECULE

• Specify information about the connectivity of single molecules

• Section path: CP2K_INPUT / FORCE_EVAL / SUBSYS / TOPOLOGY / MOL_SET / MOLECULE

• This section can be repeated.

• Subsections

  • none

• Keywords

  • CONN_FILE_FORMAT
  • CONN_FILE_NAME
  • NMOL

• Keyword descriptions

  CONN_FILE_FORMAT
  	CONN_FILE_FORMAT {Keyword}
  	Ways to determine and generate a molecules. Default is to use GENERATE
  	This keyword cannot be repeated and it expects precisely one keyword.
  	Default value: PSF
  	List of valid keywords: AMBER Use AMBER topology file for reading connectivity (compatible starting from AMBER V.7) G87 Use GROMOS G87 topology file. G96 Use GROMOS G96 topology file. GENERATE Use a simple distance criteria. (Look at keyword BONDPARM) MOL_SET Use multiple PSF (for now...) files to generate the whole system. OFF Do not generate molecules. (e.g. for QS or ill defined systems) PSF Use a PSF file to determine the connectivity. (support standard CHARMM/XPLOR and EXT CHARMM) UPSF Read a PSF file in an unformatted way (useful for not so standard PSF). USER Allows the definition of molecules and residues based on the 5th and 6th column of the COORD section. This option can be handy for the definition of molecules with QS or to save memory in the case of very large systems (use PARA_RES off).
  	Alias names for this keyword: CONNECTIVITY

  CONN_FILE_NAME
  	CONN_FILE_NAME {String}
  	Specifies the filename that contains the molecular connectivity.
  	This keyword cannot be repeated and it expects precisely one string.
  	Alias names for this keyword: CONN_FILE

  NMOL
  	NMOL {Integer}
  	number of molecules
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: 1