CHARMM c42b2 qturbo.doc



File: Qturbo -=- Node: Top
Up: (commands.doc) -=- Next: Description


        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.



File: Qturbo -=- Node: Description
Up: Top -=- Next: Usage -=- Previous: Top


        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 

=======================================================================


File: Qturbo -=- Node: Usage
Up: Top -=- Next: Installation -=- Previous: Description


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.

==============================================================================


File: Qturbo -=- Node: Installation
Up: Top -=- Next: Status -=- Previous: Usage


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>

==============================================================================

NIH Helix/Biowulf Systems
charmm.org Homepage

CHARMM Documentation / Rick_Venable@nih.gov