TOPOLOGY
Section specifying information regarding how to handle the topology for classical runs. [Edit on GitHub]
Subsections
Keywords
Keyword descriptions
- AUTOGEN_EXCLUDE_LISTS
Type: logical
Default: F
Lone keyword: T
Usage: AUTOGEN_EXCLUDE_LISTS logicalDescription: 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.
- CHARGE_BETA
Type: logical
Default: F
Aliases: CHARGE_B
Lone keyword: T
Usage: CHARGE_BETA logicalDescription: Read MM charges from the BETA field of PDB file.
- CHARGE_EXTENDED
Type: logical
Default: F
Lone keyword: T
Usage: CHARGE_EXTENDED logicalDescription: Read MM charges from the very last field of PDB file (starting from column 81). No limitations of number of digits.
- CHARGE_OCCUP
Type: logical
Default: F
Aliases: CHARGE_O
Lone keyword: T
Usage: CHARGE_OCCUP logicalDescription: Read MM charges from the OCCUP field of PDB file.
- CONN_FILE_FORMAT
Type: enum
Default: GENERATE
Aliases: CONNECTIVITY
Usage: CONN_FILE_FORMAT (PSF|UPSF|MOL_SET|GENERATE|OFF|G87|G96|AMBER|USER)Description: Ways to determine and generate a molecules. Default is to use GENERATE
Valid values:
PSFUse a PSF file to determine the connectivity. (support standard CHARMM/XPLOR and EXT CHARMM)UPSFRead a PSF file in an unformatted way (useful for not so standard PSF).MOL_SETUse multiple PSF (for now…) files to generate the whole system.GENERATEUse a simple distance criteria. (Look at keyword BONDPARM)OFFDo not generate molecules. (e.g. for QS or ill defined systems)G87Use GROMOS G87 topology file.G96Use GROMOS G96 topology file.AMBERUse AMBER topology file for reading connectivity (compatible starting from AMBER V.7)USERAllows 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).
- CONN_FILE_NAME
Type: string
Aliases: CONN_FILE
Usage: CONN_FILE_NAMEDescription: Specifies the filename that contains the molecular connectivity.
Mentions: ⭐QM/MM with Built-in Force Field
- COORD_FILE_FORMAT
Type: enum
Default: OFF
Aliases: COORDINATE
Usage: COORD_FILE_FORMAT (OFF|PDB|XYZ|G96|CRD|CIF|XTL|CP2K)Description: Set up the way in which coordinates will be read.
Valid values:
OFFCoordinates read in the &COORD section of the input filePDBCoordinates provided through a PDB file formatXYZCoordinates provided through an XYZ file formatG96Coordinates provided through a GROMOS96 file formatCRDCoordinates provided through an AMBER file formatCIFCoordinates provided through a CIF (Crystallographic Information File) file formatXTLCoordinates provided through a XTL (MSI native) file formatCP2KRead the coordinates in CP2K &COORD section format from an external file. NOTE: This file will be overwritten with the latest coordinates.
- COORD_FILE_NAME
Type: string
Aliases: COORD_FILE
Usage: COORD_FILE_NAMEDescription: Specifies the filename that contains coordinates. In case the CELL section is not set explicitly but this file contains cell information, including CIF, PDB and (Extended) XYZ formats, this file is also parsed for setting up the simulation cell.
- DISABLE_EXCLUSION_LISTS
Type: logical
Default: F
Lone keyword: T
Usage: DISABLE_EXCLUSION_LISTSDescription: Do not build any exclusion lists.
- EXCLUDE_EI
Type: enum
Default: 1-3
Usage: EXCLUDE_EI (1-1||1-2||1-3||1-4)Description: Specifies which kind of Electrostatic interaction to skip.
Valid values:
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- EXCLUDE_VDW
Type: enum
Default: 1-3
Usage: EXCLUDE_VDW (1-1||1-2||1-3||1-4)Description: Specifies which kind of Van der Waals interaction to skip.
Valid values:
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- MEMORY_PROGRESSION_FACTOR
Type: real
Default: 1.20000000E+000Description: 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.
- MOL_CHECK
Type: logical
Default: T
Lone keyword: T
Usage: MOL_CHECK logicalDescription: Check molecules have the same number of atom and names.
- MULTIPLE_UNIT_CELL
Type: integer[3]
Default: 1 1 1
Usage: MULTIPLE_UNIT_CELL 1 1 1Description: 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.
- NUMBER_OF_ATOMS
Type: integer
Default: -1
Aliases: NATOMS, NATOM
Usage: NATOMS 768000Description: Optionally define the number of atoms read from an external file (see COORD_FILE_NAME) if the COORD_FILE_FORMAT CP2K is used
- PARA_RES
Type: logical
Default: T
Lone keyword: T
Usage: PARA_RES logicalDescription: For a protein, each residue is now considered a molecule
- USE_ELEMENT_AS_KIND
Type: logical
Default: F
Lone keyword: T
Usage: USE_ELEMENT_AS_KIND logicalDescription: Kinds are generated according to the element name. Default=True for SE and TB methods.
- USE_G96_VELOCITY
Type: logical
Default: F
Lone keyword: T
Usage: USE_G96_VELOCITY logicalDescription: Use the velocities in the G96 coordinate files as the starting velocity