Keywords

• qmForces $<$ Calculate QM? $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: Turns on or off the QM calculations.

• qmParamPDB $<$ Set QM atoms $>$
  Acceptable Values: PDB file
  Description: Name of an optional secondary PDB file where the OCCupancy or BETA column has the indications for QM or MM atoms. QM atoms should have an integer bigger than zero (0) and MM atoms should have zero as the beta or occupancy field. The same file may have indications for bonds between a QM atom and an MM atom. This should be provided in case the PDB file passed to the ``coordinates" keyword already has data on its beta or occupancy columns, such as when a SMD simulations is being performed.

• qmColumn $<$ Which column? $>$
  Acceptable Values: ``beta" or ``occ"
  Description: Indicates which column has the QM/MM field. Required.

• qmSimsPerNode $<$ Sims per node $>$
  Acceptable Values: postive integer
  Default Value: 1
  Description: Number of independent simultaneous QM simulations per node.

• qmBondColumn $<$ Which bond column? $>$
  Acceptable Values: ``beta" or ``occ"
  Description: Indicates which column has the QM/MM bond information. This will tell NAMD which atoms are at the ends of a covalent bond split by the QM/MM barrier, with one atom being quantum and one being classical. There is no default value. If this parameter is provided, NAMD will parse options for dealing with QM/MM bonds.

• qmBondDist $<$ Use qmBondColumn value for distance? $>$
  Acceptable Values: ``on'' or ``off''
  Default Value: off
  Description: Indicates whether the value in the BondColumn will be used to define the distance between the QM atom and the Link Atom that will replace the MM atom in the QM system.

• qmBondValueType $<$ Does qmBondColumn value give length or ratio? $>$
  Acceptable Values: ``len'' or ``ratio''
  Default Value: len
  Description: Indicates if the values in the BondColumn represent either the length (``len'') between the QM and link atoms or the ratio (``ratio'') between the QM-MM distance and the one which will be used as the QM-Link distance.

• qmLinkElement $<$ Set link atom element $>$
  Acceptable Values: string, for example ``4 9 Cl"
  Default Value: H
  Description: User defined link atom element. Two syntaxes are allowed: if there is only one QM-MM bond, a string with the element symbol is allowed (such as ``H" or ``Cl"). If there are two or more bonds, the string needs to have the two atoms that compose the bond, and then the element (such as ``4 9 Cl"). The default element for all link atoms is hydrogen.

• qmBondScheme $<$ Select QM-MM bond scheme $>$
  Acceptable Values: ``CS" or ``RCD" or ``Z1" or ``Z2" or ``Z3"
  Default Value: CS
  Description: Indicates what will be the treatment given to QM-MM bonds in terms of charge distribution and link atom creation and placement. CS: Charge Shift Scheme; RCD: Redistributed Charge and Dipole method; Z1: Only ignored MM1 partial charge, with no charge redistribution; Z2: Ignores MM1 and all MM2 partial charges, with no charge redistribution; Z3: Ignores MM1 and all MM2 and MM3 partial charges, with no charge redistribution.

• qmElecEmbed $<$ Should point charges be used in QM? $>$
  Acceptable Values: ``on" or ``off"
  Default Value: on
  Description: Indicates if classical point charges should be used in QM calculations.

• qmSwitching $<$ Use switching on point charges? $>$
  Acceptable Values: ``on" or ``off"
  Default Value: off
  Description: This will scale down the point charges representing the classical system as to replicate the switching procedure that NAMD applies to all charged interaction (see ``switching").

• qmSwitchingType $<$ Set functional form of switching $>$
  Acceptable Values: ``switch" or ``shift"
  Default Value: shift
  Description: This option is used to decide which kind of function will be used to scale down point charges sent to QM calculations. SHIFT: This will "shift down" the entire shell of point charges so that electrostactic interactions reach zero at the cutoff distance. SWITCH: This will only change point charges in the sub-volume between the switchdist and cutoff distance, so that electrostactic interactions reach zero at the cutoff distance.

• qmPointChargeScheme $<$ Set point charge scheme $>$
  Acceptable Values: ``none" or ``round" or ``zero"
  Default Value: none
  Description: This option allows the user to decide if and how the point charges presented to the QM system will be altered. NONE: Nothing will be done. ROUND: This will change the most distant point charges so that the total sum of point charges is a whole number. ZERO: This will adjust the most distant point charges so that the total sum of point charges is 0.

• qmBaseDir $<$ Set directory for file I/O $>$
  Acceptable Values: directory path
  Description: This should be a fast read/write location, such as a RAM drive (/dev/shm on most linux distros). The user needs to make sure this directory exists in the node(s) running the QM calculation(s).

• qmReplaceAll $<$ Use only QM gradients for forces? $>$
  Acceptable Values: ``on" or ``off"
  Default Value: off
  Description: Indicates to NAMD that ALL forces form NAMD will be ignored and only the gradients from the QM software will be applied on the atoms. This IS NOT NECESSARY in any regular QM/MM simulation, and will prevent the use of any other feature from NAMD such as SMD.

• qmVdwParams $<$ Modify type names for QM atoms? $>$
  Acceptable Values: ``on" or ``off"
  Default Value: off
  Description: The QM code will change all QM atoms' van der Waals types to "q"+element (e.g., all carbons will be qC and all hydrogens will be qH) for VdW interactions. This means that a parameter file with epsilon and sigma values for these atom types must be provided along with the regular parameter files. For example, if using CHARMM force field, the new file should be in CHARMM format.

• qmPCStride $<$ Set stride for point charge $>$
  Acceptable Values: integer
  Default Value: 1
  Description: Sets a stride for new point charge determination. The same set of classical atoms will be sent to QM calculations as point charges, but with updated positions.

• qmCustomPCSelection $<$ Provide custom point charge selection? $>$
  Acceptable Values: ``on" or ``off"
  Default Value: off
  Description: Indicates that one or more file(s) will be provided with a custom selection of point charges. Each file will have a selection for a single QM group. This selection will be kept during the entire simulation.

• qmCustomPCFile $<$ File for custom point charge selection $>$
  Acceptable Values: PDB file
  Description: The file will have, in the ``qmColumn", the same QM ID provided for a single QM group. All other groups will have zero (0) in this column. In the second column (beta or occupancy), the classical or quantum atoms (from other QM regions) that need to be passed as point charges will be identified by a non-zero number.

  
  Example/Format:
  

  
  qmCustomPCFile  system/system.customPC.1.pdb 
  
  
  qmCustomPCFile  system/system.customPC.2.pdb 
  
  
  qmCustomPCFile  system/system.customPC.3.pdb 
  
  
  qmCustomPCFile  system/system.customPC.4.pdb
  

• qmLiveSolventSel $<$ Keep track of solvent? $>$
  Acceptable Values: ``on" or ``off"
  Default Value: off
  Description: With Live Solvent Selection (LSS), NAMD will automatically keep track of the solvent molecules for all QM Groups, and will exchange classical solvent molecules with QM solvent molecules every "QMLSSFreq" steps.

• qmLSSResname $<$ Set residue name for LSS $>$
  Acceptable Values: residue name
  Default Value: TIP3
  Description: Indicates which residue name will be used in LSS.

• qmLSSFreq $<$ Set frequency of LSS $>$
  Acceptable Values: integer, multiple of stepspercycle
  Default Value: 100
  Description: Frequency of LSS. Must be a multiple of stepspercycle.

• qmLSSMode $<$ How solvent molecules are selected $>$
  Acceptable Values: ``dist" or ``COM"
  Default Value: dist
  Description: For LSS, this indicates how solvent molecules are selected. In all cases, the closest solvent molecules are selected, and if a classical solvent molecule is closer than a QM one, they are swaped. DIST: This mode will use the smallest distance between a solvent atom and a non-solvent QM atom to sort solvent molecules. This is best used when the non-solvent QM atoms form irregular volumes (when the COM is not very representatve), and/or volumes with high solvent accessibility (such as a drug, or a small peptide, in solution). COM: This mode will sort solvent molecules based on Center Of Mass distance between the solvent COM and the COM of a selection for each QM group (see ``qmLSSRef" keyword). Best used with small QM regions that have limited solvent accessibility, such as an active site.

• qmLSSRef $<$ Which residues for COM of QM atoms? $>$
  Acceptable Values: string
  Description: This will indicate which residues are to be used in the determination of the COM of non-solvent QM atoms. Only these atoms will be used to determine the closest set of solvent molecules. The keyword takes a string composed of the QM group ID, the segment name and the residue ID.

  
  Example/Format:
  

  
  qmLSSRef  "1 RP1 9" 
  
  
  qmLSSRef  "2 RP1 3" 
  
  
  qmLSSRef  "2 RP1 2" 
  
  
  qmLSSRef  "3 AP1 9" 
  
  
  qmLSSRef  "3 AP1 3" 
  
  
  qmLSSRef  "4 AP1 9"
  

• qmConfigLine $<$ Pass string to QM configuration $>$
  Acceptable Values: string
  Description: The string passed to "qmConfigLine" will be copied and pasted at the very begining of the configuration file for the chosen QM software if either ORCA or MOPAC are selected.

  
  Example/Format (QM/MM NAMD-ORCA):
  

  
  qmConfigLine  "! PM3 ENGRAD" 
  
  
  qmConfigLine  "%%output PrintLevel Mini Print\[P_Mulliken\] 1 Print\[P_AtCharges_M\] 1 end"
  

  
  Example/Format (QM/MM NAMD-MOPAC):
  

  
  qmConfigLine  "PM7 XYZ T=2M 1SCF MOZYME CUTOFF=9.0 AUX LET GRAD QMMM GEO-OK" 
  
  
  qmConfigLine  "Test System"
  

• qmMult $<$ Set multiplicity of QM region $>$
  Acceptable Values: string
  Description: Multiplicity of the QM region. This is needed for proper construction of ORCA's input file. Each string must be composed of the QM region ID and its multiplicity.

  
  Example/Format:
  

  
  qmMult  "1 1" 
  
  
  qmMult  "2 1" 
  
  
  qmMult  "3 1" 
  
  
  qmMult  "4 1"
  

• qmCharge $<$ Set charge of each QM region $>$
  Acceptable Values: string
  Description: Indicates the charge of each QM region. If no charge is provided for a QM region, NAMD calculates the total charge automatically based on the given parameter set. Each string must be composed of the QM region ID and its total charge.

  
  Example/Format:
  

  
  qmCharge  "1 1" 
  
  
  qmCharge  "2 -1" 
  
  
  qmCharge  "3 1" 
  
  
  qmCharge  "4 -1"
  

• qmSoftware $<$ Which QM software? $>$
  Acceptable Values: ``mopac" or ``orca" or ``custom"
  Description: Required for QM/MM, this indicates which QM software should be used. In case the user wants to apply another QM code, this can be done by using the "custom" qmSoftware. In this case, NAMD will call the executable defined in the qmExecPath variable and will give it one argument: the full path to the input file.

  INPUT: This input file will contain on the first line the number of QM atoms (X) and the number of point charges in the file (Y, which may be 0 or more), separated by a space. The following X+Y lines will have four (4) fields: X, Y and Z coordinates, and a fourth field which will depend on the type of entry. For QM atoms, the field will contain the element of the QM atom. For point charge lines, the field will contain the charge of the point charge.

  OUTPUT: The expected output file whould be placed in the same directory as the input file, and should be named "*inputfile*.result" (meaning it will have the same path and name of the input file, plus the suffix ".result"). This file should have, on its first line, the energy of the system and the number of point charges that were passed to ORCA, and that ORCA calculated forces on (zero, if using mechanical embedding). The two numbers should be separated by a single white space. Following the standard for the INPUT file, there will be another X+Y lines in the OUTPUT file. On the following X lines (where X is the number of QM atoms passed in the input file), there must be four (4) fields: the x, y and z components of the TOTAL FORCE applied on that atom, and on the fourth field, the charge of the atom. If the user indicates that charges from the QM software should not be used (see ``qmChargeMode"), the fourth field should have zeroes, but should not be empty. On the following Y lines (where Y is the number of point charges), there must be only three (3) fields: the x, y and z components of the electrostatic force applied on that point charge. Energy should be in Kcal/mol and forces in Kcal/mol/Angstrom.

• qmExecPath $<$ Set path to QM executable $>$
  Acceptable Values: path
  Description: Required for QM/MM, this indicates the path to the QM code executable.

• qmSecProc $<$ Set path to secondary executable $>$
  Acceptable Values: path
  Description: Indicates a secondary executable that NAMD will call AFTER each QM software execution for each QM group. The executable is called with two arguments: the complete path and name of the input file used for each QM software execution; and the simulation step. This option can be used for an extra-processing at every step, e.g., for saving all QM outputs every step.

• qmPrepProc $<$ Set path to initial executable $>$
  Acceptable Values: path
  Description: Indicates an executable that must be called BEFORE the FIRST QM software execution of each QM group. The executable is called with one argument: the complete path and name of the input file used for each QM software execution. This can be used to setup a charge distribution for a molecule of interest, for example.

• qmChargeMode $<$ Set charge calculation mode $>$
  Acceptable Values: ``none" or ``mulliken" or ``chelpg"
  Default Value: mulliken
  Description: Charge calculation mode expected from the QM software. This indicates if charges should be read from the QM software and updated at every step, or if the original force field atom charges should be used. In case you are using ORCA, two charge options are allowed, Mulliken or CHELPG. We must know the kind of charge requested by the user so that the proper format is expected, read and processed. NONE: No charges are read from the QM software output and the original force field charges are preserved. MULLIKEN: This is the only other option for MOPAC and one possibility for ORCA. In case you are using the custom QM software interface, choose this option in order to use the charges calculated in the custom QM software, irrespective of the actual theory used for that calculation. CHELPG: This is a second possibility for ORCA.

• qmOutStride $<$ Set frequency of QM charge output $>$
  Acceptable Values: integer
  Default Value: 0 (not saving)
  Description: Frequency of QM charge output. A dedicated DCD file will be created to store the charge data for all QM atoms in the system. This independent frequency allows the user to store whole-system data at a larger stride to save time and space.

• qmPositionOutStride $<$ Set frequency of QM-only position output $>$
  Acceptable Values: integer
  Default Value: 0 (not saving)
  Description: Frequency of QM-only position output. A dedicated DCD file will be created to store the position data for all QM atoms in the system. This independent frequency allows the user to store whole-system data at a larger stride to save time and space.

• qmEnergyStride $<$ Set frequency of QM specific energy output $>$
  Acceptable Values: integer
  Default Value: 1
  Description: Frequency of QM-only energy output. A dedicated energy output line will be created to indicate the energy calculated by the QM code. This independent frequency allows the user to store QM-specific energy data at a larger stride to save time and space.

• qmChargeFromPSF $<$ Set charge of QM region from PSF file $>$
  Acceptable Values: ``on" or ``off"
  Default Value: off
  Description: Automatically determine charge of QM regions by adding the charges of atoms in each region.

• qmCSMD $<$ Apply conditional-SMD to QM atoms? $>$
  Acceptable Values: ``on" or ``off"
  Default Value: off
  Description: Apply conditional SMD to QM atoms in order to steer the simulation within the QM region, while avoiding bringing atoms too close together and destabilizing the molecule. C-SMD works like regular SMD, but with pairs of atoms. The first atom is pulled by a string connected to a virtual particle, and the direction of motion of the virtual particle is updated to follow a second atom. The force on the first atom will stop being applied when they come closer than a cutoff value.

• qmCSMDFile $<$ Set cSMD information $>$
  Acceptable Values: cSMD file
  Description: Name of a text file indicating pairs of atoms that will be brought closer in space. In the file, each line defines a cSMD bias, with the following syntax:
  Atom1 Atom2 Force(Kcal/Mol/A) Speed(A/step) Cutoff(A)