11.4 Q-Chem/CharmmInterface‣ Chapter 11 Molecules in Complex Environments: Solvent Models, QM/MM, QM/EFP, and Embedding Methods ‣ Q-Chem 6.2 User’s Manual

Q-Chem can be used a QM back-end for QM/MM calculations using the Charmm package. ⁵⁷² III H. L. Woodcock et al.
J. Comput. Chem.
(2007), 28, pp. 1485. Link 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 11.3.

QM/MM jobs that use the Charmm interface are controlled using the following $rem keywords:

QM_MM

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

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

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.

ESP_EFIELD

ESP_EFIELD
       Triggers the calculation of the electrostatic potential (ESP) and/or the electric field at the positions of the MM charges.
TYPE:
       INTEGER
DEFAULT:
       0
OPTIONS:
       0 Computes ESP only. 1 Computes ESP and electric field. 2 Computes electric field only.
RECOMMENDATION:
       None.

GEOM_PRINT

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

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

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

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

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

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 11.26 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. ²⁸² Das D. et al.
J. Chem. Phys.
(2002), 117, pp. 10534. Link 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. ¹³⁸⁷ Woodcock H. L. et al.
J. Chem. Phys.
(2008), 129, pp. 214109. Link 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.

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11.4 Q-Chem/Charmm Interface