A Quantum Mechanical / Molecular Mechanical (QM/MM) Interface
Between TURMOBOLE and CHARMM
Christopher N. Rowley
(cnrowley@mun.ca)
based on the Q-Chem interface from H. Lee Woodcock
(hlw@mail.usf.edu)
which was
based on the GAMESS(US) interface from Milan Hodoscek
(milan@par10.mgsl.dcrt.nih.gov,milan@kihp6.ki.si)
and
the GAMESS(UK) interface from Paul Sherwood
(p.sherwood@dl.ac.uk)
A QM/MM interface between CHARMM and the ab initio/DFT code
TURBMOLE is implemented through this module. The details of this code
and examples of its use are described in:
Riahi, S., Rowley C.N. J. Comput. Chem. 2014, DOI: 10.1002/jcc.23716
A full set of example input files can be downloaded from:
https://github.com/RowleyGroup/charmm-turbomole-examples
* Menu:
* Description:: Description of the qturbo commands.
* Usage:: How to run TURBOMOLE in CHARMM.
* Installation:: How to compile CHARMM with the TURBOMOLE interface.
The TURBOMOLE QM potential is initialized with the QTURBO command.
[SYNTAX Qturbo]
qturbo [REMOve]
REMOve: The force field terms involving the atoms designated as QM are removed.
This is needed for any QM/(MM) calculation as it it how atoms are
designated as QM atoms.
QTURBO REMOve SELEct RESId 1 END
ENERgy
=======================================================================
This interface follows the same conventions as the CHARMM/GAMESS and CHARMM/Q-Chem interfaces, where a standard CHARMM MM topology and coordinates configuration is prepared and then some atoms are designated to be modeled using QM. The location of the TURBOMOLE input files (qturboinpath), the directory where CHARMM and TURBOMOLE should write files for communication between them (qturbooutpath), and the Python wrapper script that performs the execution of TURBOMOLE (qturboexe) are specified through ENVI commands. Alternatively, these could be set in the shell environment that CHARMM is executed in envi qturboinpath "data/qturbo/" envi qturbooutpath "cquantumtest/turbodir/" envi qturboexe "../support/programs/turbo.py" For every QM/MM energy/gradient evaulation, CHARMM writes a coord file containing the coordinates of the QM atoms. The TURBOMOLE execution script is then run by CHARMM, which copies this file to a temporary directory along with the neccessary TURBOMOLE input files from qturboinpath (control, mos, mos.bin, basis, auxbasis...). If there are MM atoms present, the location and magnitude of these charges will be written to the file pc_charges. Depending on whether the jobtype is a DFT calculation or an ab initio method, ridft/rdgrad or dscf/ricc2 are then executed by Python wrapper script, qturboexe. TURBOMOLE will generate a file containing the forces on the QM atoms (gradient) and the gradient on the point charges due to the QM region (pc_gradient). These files are copied back to qturbooutpath by the wrapper script. The wrapper script then exits and CHARMM will read in the gradient files and continue the calculation. The files in qturboinpath must be configured by the user using the TURBOMOLE define program before the execution of CHARMM. See the TURBOMOLE manual for instructions on how to do this. ==============================================================================
To use the CHARMM TURBOMOLE interface, CHARMM must be compiled with the QTURBO keyword, which is invoked by the command: install.com <machine-type> <CHARMM size> QT <other CHARMM options> ==============================================================================
CHARMM Documentation / Rick_Venable@nih.gov