Q-Chem can be used a QM back-end for QM/MM calculations using Charmm package.[III et al.(2007)III, Hodoscek, Gilbert, Gill, Schaefer III, and Brooks] In this case, both software packages are required to perform the calculations, but all the code required for communication between the programs is incorporated in the released versions. Stand-alone QM/MM calculations are described in Section 12.3.
QM/MM jobs that use the Charmm interface are controlled using the following $rem keywords:
QM_MM
Turns on the Q-Chem/Charmm interface.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Do QM/MM calculation through the Q-Chem/Charmm interface.
FALSE
Turn this feature off.
RECOMMENDATION:
Use the default unless running calculations with Charmm.
QMMM_PRINT
Controls the amount of output printed from a QM/MM job.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Limit molecule, point charge, and analysis printing.
FALSE
Normal printing.
RECOMMENDATION:
Use the default unless running calculations with Charmm.
QMMM_CHARGES
Controls the printing of QM charges to file.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Writes a charges.dat file with the Mulliken charges from the QM region.
FALSE
No file written.
RECOMMENDATION:
Use the default unless running calculations with Charmm where charges on the QM region need to be saved.
IGDEFIELD
Triggers the calculation of the electrostatic potential and/or the electric field at the positions of the MM charges.
TYPE:
INTEGER
DEFAULT:
UNDEFINED
OPTIONS:
O
Computes ESP.
1
Computes ESP and EFIELD.
2
Computes EFIELD.
RECOMMENDATION:
Must use this $rem when IGDESP is specified.
GEOM_PRINT
Controls the amount of geometric information printed at each step.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Prints out all geometric information; bond distances, angles, torsions.
FALSE
Normal printing of distance matrix.
RECOMMENDATION:
Use if you want to be able to quickly examine geometric parameters at the beginning and end of optimizations. Only prints in the beginning of single point energy calculations.
QMMM_FULL_HESSIAN
Trigger the evaluation of the full QM/MM Hessian.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Evaluates full Hessian.
FALSE
Hessian for QM-QM block only.
RECOMMENDATION:
None
LINK_ATOM_PROJECTION
Controls whether to perform a link-atom projection
TYPE:
LOGICAL
DEFAULT:
TRUE
OPTIONS:
TRUE
Performs the projection
FALSE
No projection
RECOMMENDATION:
Necessary in a full QM/MM Hessian evaluation on a system with link atoms
HESS_AND_GRAD
Enables the evaluation of both analytical gradient and Hessian in a single job
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Evaluates both gradient and Hessian.
FALSE
Evaluates Hessian only.
RECOMMENDATION:
Use only in a frequency (and thus Hessian) evaluation.
GAUSSIAN_BLUR
Enables the use of Gaussian-delocalized external charges in a QM/MM calculation.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
Delocalizes external charges with Gaussian functions.
FALSE
Point charges
RECOMMENDATION:
None
SKIP_CHARGE_SELF_INTERACT
Ignores the electrostatic interactions among external charges in a QM/MM calculation.
TYPE:
LOGICAL
DEFAULT:
FALSE
OPTIONS:
TRUE
No electrostatic interactions among external charges.
FALSE
Computes the electrostatic interactions among external charges.
RECOMMENDATION:
None
Example 12.302 Do a basic QM/MM optimization of the water dimer. You need Charmm to do this but this is the Q-Chem file that is needed to test the QM/MM functionality. These are the bare necessities for a Q-Chem/Charmm QM/MM calculation.
$molecule
0 1
O -0.91126 1.09227 1.02007
H -1.75684 1.51867 1.28260
H -0.55929 1.74495 0.36940
$end
$rem
METHOD hf ! HF Exchange
BASIS cc-pvdz ! Correlation Consistent Basis
QM_MM true ! Turn on QM/MM calculation
JOBTYPE force ! Need this for QM/MM optimizations
$end
$external_charges
1.20426 -0.64330 0.79922 -0.83400
1.01723 -1.36906 1.39217 0.41700
0.43830 -0.06644 0.91277 0.41700
$end
The Q-Chem/Charmm interface is unique in that:
The external point charges can be replaced with Gaussian-delocalized charges with a finite width.[Das et al.(2002)Das, Eurenius, Billings, Sherwood, Chatfield, Hodoscek, and Brooks] This is an empirical way to include the delocalized character of the electron density of atoms in the MM region. This can be important for the electrostatic interaction of the QM region with nearby atoms in the MM region.
We allow the evaluation of the full QM/MM Hessian.[Woodcock et al.(2008)Woodcock, Zheng, Ghysels, Shao, Kong, and Brooks] When link atoms are inserted to saturate the QM region, all Hessian elements associated with link atoms are automatically projected onto their QM and MM host atoms.
For systems with a large number of MM atoms, one can define blocks consisting of multiple MM atoms (i.e., mobile blocks) and efficiently evaluate the corresponding mobile-block Hessian (MBH) for normal mode analysis.