QM/MM parameters¶
The QM/MM interface parameters define the interaction between classical and quantum regions.
qmmm
[ [eref] <double precision default 0.0d0>]
[ [bqzone] <double precision default 9.0d0>]
[ [mm_charges] [exclude <(nonealllinkbondlinkbond_H) default none>]
[ expand <noneallsolutesolvent> default none]
[ update <integer default 0>]
[ [link_atoms] <(hydrogenhalogen) default hydrogen>]
[ [link_ecp] <(autouser) default auto>]
[ [region] < [region1] [region2] [region3] > ]
[ [method] [method1] [method2] [method3] ]
[ [maxiter] [maxiter1] [maxiter2] [maxiter3] ]
[ [ncycles] < [number] default 1 > ]
[ [density] [espfit] [static] [dynamical] ]
[ [xyz] ]
[ [convergence] <double precision default 1.0d4>] ]
[ [load] ]
[ [nsamples] ]
end
Detailed explanation of the subdirectives in the QM/MM input block is given below:
QM/MM eref¶
eref <double precision default 0.0d0>
This directive sets the relative zero of energy for the QM component of
the system. The need for this directive arises from different
definitions of zero energy for QM and MM methods. In QM methods the zero
of energy for the system is typically vacuum. The zero of energy for the
MM system is by definition of most parameterized force fields the
separated atom energy. Therefore in many cases the energetics of the QM
system will likely overshadow the MM component of the system. This
imbalance can be corrected by suitably chosen value of eref
. In most
cases IT IS OK to leave eref
at its default value of zero.
QM/MM bqzone¶
bqzone <double precision default 9.0d0>
This directive defines the radius of the zone (in angstroms) around the quantum region where classical residues/segments will be allowed to interact with quantum region both electrostatically and through Van der Waals interactions. It should be noted that classical atoms interacting with quantum region via bonded interactions are always included (this is true even if bqzone is set to 0). In addition, even if one atom of a given charged group is in the bqzone (residues are typically treated as one charged group) then the whole group will be included.
QM/MM mm_charges¶
mm_charges [exclude <(nonealllinkbondlinkbond_H) default none>]
[expand <noneallsolutesolvent> default none]
[update <integer default 0>]
This directive controls treatment of classical point (MM) charges that are interacting with QM region. For most QM/MM applications the use of directive will be not be necessary. Its absence would be simply mean that all MM charges within the cuttof distance ( as specified by cutoff ) as well those belonging to the charges groups directly bonded to QM region will be allowed to interact with QM region.
Keyword exclude
specifies the subset MM charges that will be
specifically excluded from interacting with QM region.
none
default value reverts to the original set of MM charges as described above.all
excludes all MM charges from interacting with QM region (“gas phase” calculation).linkbond
excludes MM charges that are connected to a quantum region by at most two bonds,linkbond_H
similar tolinkbond
but excludes only hydrogen atoms.
Keyword expand
expands the set MM charges interacting with QM region
beyond the limits imposed by cutoff value.
none
default value reverts to the original set of MM chargessolute
expands electrostatic interaction to all solute MM chargessolvent
expands electrostatic interaction to all solvent MM chargesall
expands electrostatic interaction to all MM charges
Keyword update
specifies how often list of MM charges will be updated in
the course of the calculation. Default behavior is not to update.
QM/MM link_atoms¶
link_atoms <(hydrogenhalogen) default halogen>
This directive controls the treatment of bonds crossing the boundary between quantum and classical regions. The use of hydrogen keyword will trigger truncation of such bonds with hydrogen link atoms. The position of the hydrogen atom will be calculated from the coordinates of the quantum and classical atom of the truncated bond using the following expression
where g is the scale factor set at 0.709
Setting link_atoms
to halogen
will result in the modification of the
quantum atom of the truncated bond to the fluoride atom. This
fluoride atom will typically carry an effective core potential (ECP)
basis set as specified in link_ecp
directive.
QM/MM link_ecp¶
link_ecp <(autouser)default auto>
This directive specifies ECP basis set on fluoride link atoms. If set to
auto
the ECP basis set given by Zhang, Lee, Yang^{1} for 631G basis
will be used. Strictly speaking, this implies the use of 631G
spherical basis as the main basis set. If other choices are desired then
keyword user should be used and ECP basis set should be entered
separatelly following the format given in section dealing with ECPs .
The name tag for fluoride link atoms is F_L
.
QM/MM region¶
region < [region1] [region2] [region3] >
This directive specifies active region(s) for optimization, dynamics, frequency, and free energy calculations. Up to three regions can be specified, those are limited to
qm
 all quantum atomsqmlink
 quantum and link atomsmm_solute
 all classical solute atoms excluding link atomssolute
 all solute atoms including quantumsolvent
all solvent atomsmm
all classical solute and solvent atoms, excluding link atomsall
all atoms
Only the first region will be used in dynamics, frequency, and free energy calculations. In the geometry optimizations, all three regions will be optimized using the following optimization methods
if (region.eq."qm") then
method = "bfgs"
else if (region.eq."qmlink") then
method = "bfgs"
else if (region.eq."mm_solute") then
method = "lbfgs"
else if (region.eq."mm") then
method = "sd"
else if (region.eq."solute") then
method = "sd"
else if (region.eq."solvent") then
method = "sd"
else if (region.eq."all") then
method = "sd"
end if
where “bfgs” stands for Broyden–Fletcher–Goldfarb–Shanno (BFGS) optimization method, “lbfgs” limited memory version of quasinewton, and “sd” simple steepest descent algorithm. These assignments can be potentially altered using method directive.
QM/MM method¶
method [method1] [method2] [method3]
This directive controls which optimization algorithm will be used for the regions as defined by [[qmmm_regionQmmm_region]] directive.
The allowed values are bfgs
aka DRIVER,
lbfgs
limited memory version of quasinewton,
and sd
simple steepest descent algorithm.
The use of this directive is not recommended in all but special cases. In particular,
bfgs
should be used for QM region if there are any constraints,
sd
method should always be used for classical solute and solvent atoms with shake constraints.
QM/MM maxiter¶
maxiter [maxiter1] [maxiter2] [maxiter3]
This directive controls maximum number of iterations for the optimizations of regions as defined by by regions directive. User is strongly encouraged to set this directive explicitly as the default value shown below may not be appropriate in all the cases:
if(region.eq."qm") then
maxiter = 20
else if (region.eq."qmlink") then
maxiter = 20
else if (region.eq."mm") then
maxiter = 100
else if (region.eq."solvent") then
maxiter = 100
else
maxiter = 50
end if
QM/MM ncycles¶
ncycles < [number] default 1 >
This directive controls the number of optimization cycles where the defined regions will be optimized in succession, or number of sampling cycles in free energy calculations.
QM/MM density¶
density [espfit] [static] [dynamical] default dynamical
This directive controls the electrostatic representation of fixed QM region during optimization/dynamics of classical regions. It has no effect when position of QM atoms are changing.

dynamical is an option where QM region is treated the standard way, through the recalculation of the wavefunction calculated and the resulting electron density is used to compute electrostatic interactions with classical atoms. This option is the most expensive one and becomes impractical for large scale optimizations.

static option will not recalculate QM wavefunction but will still use full electron density in the computations of electrostatic interactions.

espfit option will not recalculate QM wavefunction nor it will use full electron density. Instead, a set of ESP charges for QM region will be calculated and used to compute electrostatic interactions with the MM regions. This option is the most efficient and is strongly recommended for large systems.
Note that both “static” and “espfit” options do require the presence of the movecs file. It is typically available as part as part of calculation process. Otherwise it can be generated by running qmmm energy calculation.
In most calculations default value for density would dynamical, with the exception of free energy calculations where default setting espfit will be used.
QM/MM load¶
load < esp > [<filename>]
This directive instructs to load external file (located in permanent directory) containing esp charges for QM region. If filename is not provided it will be constructed from the name of the restart file by replacing “.rst” suffix with “.esp”. Note that file containing esp charges is always generated whenever esp charge calculation is performed
QM/MM convergence¶
convergence < double precision etol default 1.0d4>
This directive controls convergence of geometry optimization. The optimization is deemed converged if absolute difference in total energies between consecutive optimization cycles becomes less than etol.
QM/MM nsamples¶
nsamples
This directive is required for free energy calculations and defines number of samples for averaging during single cycle.
References¶

Zhang, Y.; Lee, T.S.; Yang, W. A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods. The Journal of Chemical Physics 1999, 110 (1), 46–54. https://doi.org/10.1063/1.478083. ↩