Section TOPOLOGY

• Section specifying information regarding how to handle the topology for classical runs.

• Section path: CP2K_INPUT / FORCE_EVAL / SUBSYS / TOPOLOGY

• This section cannot be repeated.

• Subsections

  • CENTER_COORDINATES
  • DUMP_PDB
  • DUMP_PSF
  • EXCLUDE_EI_LIST
  • EXCLUDE_VDW_LIST
  • GENERATE
  • MOL_SET

• Keywords

  • AUTOGEN_EXCLUDE_LISTS
  • CHARGE_BETA
  • CHARGE_EXTENDED
  • CHARGE_OCCUP
  • CONN_FILE_FORMAT
  • CONN_FILE_NAME
  • COORD_FILE_FORMAT
  • COORD_FILE_NAME
  • DISABLE_EXCLUSION_LISTS
  • EXCLUDE_EI
  • EXCLUDE_VDW
  • MEMORY_PROGRESSION_FACTOR
  • MOL_CHECK
  • MULTIPLE_UNIT_CELL
  • NUMBER_OF_ATOMS
  • PARA_RES
  • USE_G96_VELOCITY

• Keyword descriptions

  AUTOGEN_EXCLUDE_LISTS
  	AUTOGEN_EXCLUDE_LISTS {Logical}
  	When True, the exclude lists are solely based on the bond data in the topology. The (minimal) number of bonds between two atoms is used to determine if the atom pair is added to an exclusion list. When False, 1-2 exclusion is based on bonds in the topology, 1-3 exclusion is based on bonds and bends in the topology, 1-4 exclusion is based on bonds, bends and dihedrals in the topology. This implies that a missing dihedral in the topology will cause the corresponding 1-4 pair not to be in the exclusion list, in case 1-4 exclusion is requested for VDW or EI interactions.
  	This keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  CHARGE_BETA
  	CHARGE_BETA {Logical}
  	Read MM charges from the BETA field of PDB file.
  	This keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.
  	Alias names for this keyword: CHARGE_B

  CHARGE_EXTENDED
  	CHARGE_EXTENDED {Logical}
  	Read MM charges from the very last field of PDB file (starting from column 81). No limitations of number of digits.
  	This keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  CHARGE_OCCUP
  	CHARGE_OCCUP {Logical}
  	Read MM charges from the OCCUP field of PDB file.
  	This keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.
  	Alias names for this keyword: CHARGE_O

  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: GENERATE
  	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 sytem. 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

  COORD_FILE_FORMAT
  	COORD_FILE_FORMAT {Keyword}
  	Set up the way in which coordinates will be read.
  	This keyword cannot be repeated and it expects precisely one keyword.
  	Default value: OFF
  	List of valid keywords: CIF Coordinates provided through a CIF (Crystallographic Information File) file format CP2K Read the coordinates in CP2K &COORD section format from an external file. NOTE: This file will be overwritten with the latest coordinates. CRD Coordinates provided through an AMBER file format G96 Coordinates provided through a GROMOS96 file format OFF Coordinates read in the &COORD section of the input file PDB Coordinates provided through a PDB file format XTL Coordinates provided through a XTL (MSI native) file format XYZ Coordinates provided through an XYZ file format
  	Alias names for this keyword: COORDINATE

  COORD_FILE_NAME
  	COORD_FILE_NAME {String}
  	Specifies the filename that contains coordinates.
  	This keyword cannot be repeated and it expects precisely one string.
  	Alias names for this keyword: COORD_FILE

  DISABLE_EXCLUSION_LISTS
  	DISABLE_EXCLUSION_LISTS {Logical}
  	Do not build any exclusion lists.
  	This keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  EXCLUDE_EI
  	EXCLUDE_EI {Keyword}
  	Specifies which kind of Electrostatic interaction to skip.
  	This keyword cannot be repeated and it expects precisely one keyword.
  	Default value: 1-3
  	List of valid keywords: 1-1 Without description, yet. 1-2 Without description, yet. 1-3 Without description, yet. 1-4 Without description, yet.

  EXCLUDE_VDW
  	EXCLUDE_VDW {Keyword}
  	Specifies which kind of Van der Waals interaction to skip.
  	This keyword cannot be repeated and it expects precisely one keyword.
  	Default value: 1-3
  	List of valid keywords: 1-1 Without description, yet. 1-2 Without description, yet. 1-3 Without description, yet. 1-4 Without description, yet.

  MEMORY_PROGRESSION_FACTOR
  	MEMORY_PROGRESSION_FACTOR {Real}
  	This keyword is quite technical and should normally not be changed by the user. It affects the memory allocation during the construction of the topology. It does NOT affect the memory used once the topology is built.
  	This keyword cannot be repeated and it expects precisely one real.
  	Default value: 1.20000000E+000

  MOL_CHECK
  	MOL_CHECK {Logical}
  	Check molecules have the same number of atom and names.
  	This keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .TRUE.

  MULTIPLE_UNIT_CELL
  	MULTIPLE_UNIT_CELL {Integer} {Integer} {Integer}
  	Specifies the numbers of repetition in space (X, Y, Z) of the defined cell, assuming it as a unit cell. This keyword affects only the coordinates specification. The same keyword in SUBSYS%CELL%MULTIPLE_UNIT_CELL should be modified in order to affect the cell specification.
  	This keyword cannot be repeated and it expects precisely 3 integers.
  	Default values: 1 1 1

  NUMBER_OF_ATOMS
  	NUMBER_OF_ATOMS {Integer}
  	Optionally define the number of atoms read from an external file (see COORD_FILE_NAME) if the COORD_FILE_FORMAT CP2K is used
  	This keyword cannot be repeated and it expects precisely one integer.
  	Default value: -1
  	Alias names for this keyword: NATOMS, NATOM

  PARA_RES
  	PARA_RES {Logical}
  	For a protein, each residue is now considered a molecule
  	This keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .TRUE.

  USE_G96_VELOCITY
  	USE_G96_VELOCITY {Logical}
  	Use the velocities in the G96 coordinate files as the starting velocity
  	This keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.