The CP2K project : input section TOPOLOGY

Section TOPOLOGY

Index of all sections. This section is located at __ROOT__%FORCE_EVAL%SUBSYS%TOPOLOGY.

Section specifying information regarding how to handle the topology for classical runs. This section can not be repeated and can be optional.

Subsections

Section keywords

Keyword descriptions

CHARGE_OCCUP
CHARGE_OCCUP logical
Read MM charges from the OCCUP field of PDB file.
This optional keyword expects a logical
This keyword behaves as a switch T . Default value: F
variants: CHARGE_O
CHARGE_BETA
CHARGE_BETA logical
Read MM charges from the BETA field of PDB file.
This optional keyword expects a logical
This keyword behaves as a switch T . Default value: F
variants: 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 optional keyword expects a logical
This keyword behaves as a switch T . Default value: F
PARA_RES
PARA_RES logical
For a protein, each residue is now considered a molecule
This optional keyword expects a logical
This keyword behaves as a switch T . Default value: T
MOL_CHECK
MOL_CHECK logical
Check molecules have the same number of atom and names.
This optional keyword expects a logical
This keyword behaves as a switch T . Default value: T
USE_G96_VELOCITY
USE_G96_VELOCITY logical
Use the velocities in the G96 coordinate files as the starting velocity
This optional keyword expects a logical
This keyword behaves as a switch T . Default value: F
COORD_FILE_NAME
COORD_FILE_NAME
Specifies the filename that contains coordinates.
This required keyword expects a string
variants: COORD_FILE
COORD_FILE_FORMAT
COORD_FILE_FORMAT (OFF|PDB|XYZ|G96|CRD|CIF|XTL)
Set up the way in which coordinates will be read.
This optional keyword expects a keyword. Default value: OFF
valid keywords:
  • OFF: Coordinates read in the &COORD section of the input file
  • PDB: Coordinates provided through a PDB file format
  • XYZ: Coordinates provided through an XYZ file format
  • G96: Coordinates provided through a GROMOS96 file format
  • CRD: Coordinates provided through an AMBER file format
  • CIF: Coordinates provided through a CIF (Crystallographic Information File) file format
  • XTL: Coordinates provided through a XTL (MSI native) file format
variants: COORDINATE
CONN_FILE_NAME
CONN_FILE_NAME
Specifies the filename that contains the molecular connectivity.
This required keyword expects a string
variants: CONN_FILE
CONN_FILE_FORMAT
CONN_FILE_FORMAT (PSF|UPSF|MOL_SET|GENERATE|OFF|G87|G96|AMBER)
Ways to determine and generate a molecules. Default is to use GENERATE
This optional keyword expects a keyword. Default value: GENERATE
valid keywords:
  • 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).
  • MOL_SET: Use multiple PSF (for now...) files to generate the whole sytem.
  • GENERATE: Use a simple distance criteria. (Look at keyword BONDPARM)
  • OFF: Do not generate molecules. (Use for QS or ill defined systems)
  • G87: Use GROMOS G87 topology file.
  • G96: Use GROMOS G96 topology file.
  • AMBER: Use AMBER topology file for reading connectivity (compatible starting from AMBER V.7)
variants: CONNECTIVITY
EXCLUDE_VDW
EXCLUDE_VDW (1-2||1-3||1-4)
Specifies which kind of Van der Waals interaction to skip.
This optional keyword expects a keyword. Default value: 1-3
valid keywords: 1-2, 1-3, 1-4
EXCLUDE_EI
EXCLUDE_EI (1-2||1-3||1-4)
Specifies which kind of Electrostatic interaction to skip.
This optional keyword expects a keyword. Default value: 1-3
valid keywords: 1-2, 1-3, 1-4
CENTER_COORDINATES
CENTER_COORDINATES logical
Center the molecules in the computational box.
This optional keyword expects a logical
This keyword behaves as a switch T . Default value: F
MULTIPLE_UNIT_CELL
MULTIPLE_UNIT_CELL 1 1 1
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 optional keyword expects precisely 3 integers. Default value: 1 1 1


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