List of keywords in the &QMMM section

Mandatory keywords:

COORDINATES

Section: &QMMM

On the next line the name of a Gromos96 format coordinate http has to be given. Note, that this http must match the corresponding input and topology https. Note, that in case of hydrogen capping, this http has to be modified to also contain the respective dummy hydrogen atoms.

INPUT

Section: &QMMM

On the next line the name of a Gromos input http has to be given. A short summary of the input http syntax and some keywords are in section 11.6.2. Note, that it has to be a correct input http, even though many options do not apply for QM/MM runs.

TOPOLOGY

Section: &QMMM

On the next line the name of a Gromos topology http has to be given. Regardless of the force field, this topology http has to be in Gromos format[129]. Topologies created with Amber can be converted using the respective conversion tools shipped with the interface code. A short summary of the topology http syntax and some keywords are in section 11.6.2.

Other keywords:

ADD_HYDROGEN

Section: &QMMM

This keyword is used to add hydrogens to the QM system if a united atom topology is used (like in Gromos). On the next line the number of atoms to be ``hydrogenized'' has to be given and in the line following that, the corresponding gromos atom numbers. A number of hydrogens consistent with the hybridization of the ``hydrogenized'' carbons are added.

AMBER

Section: &QMMM

An Amber functional form for the classical force field is used. In this case coordinates and topology https as obtained by Amber have to be converted in Gromos format just for input/read consistency. This is done with the tool amber2gromos available with the CPMD/QMMM package.
This keyword is mutually exclusive with the GROMOS keyword (which is used by default).

ARRAYSIZES

Section: &QMMM

Parameters for the dimensions of various internal arrays can be given in this block. The syntax is one label and the according dimension per line. The suitable parameters can be estimated using the script estimate_gromos_size bundled with the QM/MM-code distribution. Example:

 ARRAYSIZES
   MAXATT 20
   MAXAA2 17
   MXEX14 373
 END ARRAYSIZES

This section of the input has to be terminated by a line containing END VELOCITIES.

BOX TOLERANCE

Section: &QMMM

The value for the box tolerance is read from the next line. In a QM/MM calculation the size of the QM-box is fixed and the QM-atoms must not come to close to the walls of this box. On top of always recentering the QM-box around the center of the distribution of the atoms, CPMD prints a warning message to the output when the distribution extends too much to fit into the QM-box properly anymore. This value may need to be adjusted to the requirements of the Poisson solver used (see section 9.4).
Default value is 8 a.u.

BOX WALLS

Section: &QMMM

The thickness parameter for soft, reflecting QM-box walls is read from the next line. In contrast to the normal procedure of re-centering the QM-box, a soft, reflecting confinement potential is applied if atoms come too close to the border of the QM box [204]. It is highly recommended to also use SUBTRACT COMVEL in combination with this feature. NOTE: to have your QM-box properly centered, it is best to run a short MD with this feature turned off and then start from the resulting restart with the soft walls turned on. Since the reflecting walls reverse the sign of the velocities, $\mathbf{p}_I \to -\mathbf{p}_I$ ($I$ = QM atom index), be aware that this options affects the momentum conservation in your QM subsystem.
This feature is disabled by default

CAPPING

Section: &QMMM

Add (dummy) hydrogen atoms to the QM-system to saturate dangling bonds when cutting between MM- and QM-system. This needs a special pseudopotential entry in the &ATOMS section (see section 9.16.7 for more details).

CAP_HYDROGEN

Section: &QMMM

same as CAPPING.

ELECTROSTATIC COUPLING [LONG RANGE]

Section: &QMMM

The electrostatic interaction of the quantum system with the classical system is explicitly kept into account for all classical atoms at a distance $r \leq$  RCUT_NN from any quantum atom and for all the MM atoms at a distance of RCUT_NN $< r \leq$  RCUT_MIX and a charge larger than $0.1 e_0$ (NN atoms).

MM-atoms with a charge smaller than $0.1 e_0$ and a distance of RCUT_NN $< r \leq$  RCUT_MIX and all MM-atoms with RCUT_MIX $< r \leq$  RCUT_ESP are coupled to the QM system by a ESP coupling Hamiltonian (EC atoms).

If the additional LONG RANGE keyword is specified, the interaction of the QM-system with the rest of the classical atoms is explicitly kept into account via interacting with a multipole expansion for the QM-system up to quadrupolar order. A http named MULTIPOLE is produced.

If LONG RANGE is omitted the quantum system is coupled to the classical atoms not in the NN-area and in the EC-area list via the force-field charges.

If the keyword ELECTROSTATIC COUPLING is omitted, all classical atoms are coupled to the quantum system by the force-field charges (mechanical coupling).

The https INTERACTING.pdb, TRAJECTORY_INTERACTING, MOVIE_INTERACTING, TRAJ_INT.dcd, and ESP (or some of them) are created. The list of NN and EC atoms is updated every 100 MD steps. This can be changed using the keyword UPDATE LIST.

The default values for the cut-offs are RCUT_NN=RCUT_MIX=RCUT_ESP=10 a.u.. These values can be changed by the keywords RCUT_NN, RCUT_MIX, and RCUT_ESP with $r_{nn} \leq r_{mix} \leq r_{esp}$ .

ESPWEIGHT

Section: &QMMM

The ESP-charg fit weighting parameter is read from the next line.
Default value is $0.1 e_0$ .

EXCLUSION {GROMOS,LIST}

Section: &QMMM

Specify charge interactions that should be excluded from the QM/MM hamiltonian. With the additional flag GROMOS, the exclusions from the Gromos topology are used. With the additional flag LIST an explicit list is read from following lines. The format of that list has the number of exclusions in the first line and then the exclusions listed in pairs of the QM-atom number and the MM-atom in Gromos ordering.

FLEXIBLE WATER [ALL,BONDTYPE]

Section: &QMMM

Convert some solvent water molecules into solute molecules and thus using a flexible potential.
With the BONDTYPE flag, the three bond potentials (OH1, OH2, and H1H2) can be given as index in the BONDTYPE section of the Gromos topology http. Note that the non-bonded parameters are taken from the SOLVENATOM section of the TOPOLOGY http. Default is to use the values: 35, 35, 41.
With the additional flag ALL this applies to all solvent water molecules, otherwise on the next line the number of flexible water molecules has to be given with the Gromos index numbers of their respective Oxygen atoms on the following line(s).
On successful conversion a new, adapted topology http, MM_TOPOLOGY, is written that has to be used with the TOPOLOGY keyword for subsequent restarts. Also the INPUT http has to be adapted: in the SYSTEM section the number of solvent molecules has to be reduced by the number of converted molecules, and in the SUBMOLECULES section the new solute atoms have to be added accordingly.
Example:

     FLEXIBLE WATER BONDTYPE
      4 4 5
      26
        32   101   188   284   308   359   407   476   506   680
       764   779   926  1082  1175  1247  1337  1355  1607  1943
      1958  1985  2066  2111  2153  2273

GROMOS

Section: &QMMM

A Gromos functional form for the classical force field is used (this is the default).
This keyword is mutually exclusive with the AMBER keyword.

HIRSHFELD [ON,OFF]

Section: &QMMM

With this option, restraints to Hirshfeld charges [143] can be turned on or off
Default value is ON.

MAXNN

Section: &QMMM

Then maximum number of NN atoms, i.e. the number of atoms coupled to the QM system via ELECTROSTATIC COUPLING is read from the next line. (Note: This keyword was renamed from MAXNAT in older versions of the QM/MM interface code to avoid confusion with the MAXNAT keyword in the ARRAYSIZES block.)
Default value is 5000.

NOSPLIT

Section: &QMMM

If the program is run on more than one node, the MM forces calculation is performed on all nodes. Since the MM part is not parallelized, this is mostly useful for systems with a small MM-part and for runs using only very few nodes. Usually the QM part of the calculation needs the bulk of the cpu-time in the QM/MM.
This setting is the default. See also under SPLIT.

RCUT_NN

Section: &QMMM

The cutoff distance for atoms in the nearest neighbor region from the QM-system ( $r \leq r_{nn}$ ) is read from the next line. (see ELECTROSTATIC COUPLING for more details).
Default value is 10 a.u.

RCUT_MIX

Section: &QMMM

The cutoff distance for atoms in the intermediate region ( $r_{nn} < r \leq r_{mix}$ ) is read from the next line. (see ELECTROSTATIC COUPLING for more details).
Default value is 10 a.u.

RCUT_ESP

Section: &QMMM

The cutoff distance for atoms in the ESP-area ( $r_{mix} < r \leq r_{esp}$ ) is read from the next line. (see ELECTROSTATIC COUPLING for more details).
Default value is 10 a.u.

RESTART TRAJECTORY [FRAME {num},FILE '{fname}',REVERSE]

Section: &QMMM

Restart the MD with coordinates and velocities from a previous run. With the additional flag FRAME followed by the frame number the trajectory frame can be selected. With the flag FILE followed by the name of the trajectory http, the filename can be set (Default is TRAJECTORY). Finally the flag REVERSE will reverse the sign of the velocities, so the system will move backwards from the selected point in the trajecory.

SAMPLE INTERACTING [OFF,DCD]

Section: &QMMM

The sampling rate for writing a trajectory of the interacting subsystem is read from the next line. With the additional keyword OFF or a sampling rate of 0, those trajectories are not written. The coordinates of the atoms contained in the http INTERACTING.pdb are written, in the same order, on the http TRAJECTORY_INTERACTING every. If the MOVIE output is turned on, a http MOVIE_INTERACTING is written as well. With the additional keyword DCD the http TRAJ_INT.dcd is also written to. if the sampling rate is negative, then only the TRAJ_INT.dcd is written.
Default value is 5 for MD calculations and OFF for others.

SPLIT

Section: &QMMM

If the program is run on more than one node, the MM forces calculation is performed on a separate node. This is mostly useful for systems with a large MM-part and runs with many nodes where the accumulated time used for the classical part has a larger impact on the performance than losing one node for the (in total) much more time consuming QM-part.
Default is NOSPLIT.

TIMINGS

Section: &QMMM

Display timing information about the various parts of the QM/MM interface code in the output http. Also a file TIMINGS with even more details is written. This option is off by default.

UPDATE LIST

Section: &QMMM

On the next line the number of MD steps between updates of the various lists of atoms for ELECTROSTATIC COUPLING is given. At every list update a http INTERACTING_NEW.pdb is created (and overwritten).

Default value is 100.

VERBOSE

Section: &QMMM

The progress of the QM/MM simulation is reported more verbosely in the output. This option is off by default.

WRITE LOCALTEMP [STEP {nfi_lt}]

Section: &QMMM

The Temperatures of the QM subsystem, the MM solute (without the QM atoms) and the solvent (if present) are calculated separately and written to the standard output and a http QM_TEMP. The http has 5 columns containing the QM temperature, the MM temperature, the solvent temperature (or 0.0 if the solvent is part of the solute), and the total temperature in that order. With the optional parameters STEP followed by an integer, this is done only every nfi_lt timesteps.