CHARMM c30b1 sccdftb.doc

File: SCCDFTB ]-[ Node: Top
Up: (commands.doc) -=- Next: Description\n

      Combined Quantum Mechanical and Molecular Mechanics Method
                       Based on SCCDFTB in CHARMM

                     by  Qiang Cui and Marcus Elstner

        The approximate Density Functional program SCCDFTB (Self-
consistent charge Density-Functional Tight-Binding) is interfaced with
CHARMM program in a QM/MM method.  

	This method is described in 

Phys. Rev. B  58 (1998) 7260,
Phys. Stat. Sol. B 217 (2000) 357,
J. Phys. : Condens. Matter.  14 (2002) 3015.

	The QM/MM interface in CHARMM has been described in
J. Phys. Chem. B 105 (2001) 569

* Menu:

* Description::         Description of the sccdftb commands.
* Usage::               How to run sccdftb in CHARMM.
* Installation::        How to install sccdftb in CHARMM environment.
* Status::              Status of the interface code.

File: SCCDFTB Node: Description ]-[ Up: Top
Next: Usage -=- Previous: Top\n

     The SCCDFTB QM potential is initialized with the SCCDFTB command


SCCDFTB   [REMOve] [CHRG] (atom selection) [TEMPerature] [SCFtolerance]

REMOve:  Classical energies within QM atoms are removed.

CHRG:    Net charge in the QM subsystem.

         The atoms in selection will be treated as QM atoms.

TEMPerature:  Specifies the electronic temperature (Fermi distribution).
              Can be used to accelerate or achieve SCF convergence 
              (default =0.0).
SCFtolerance: Convergence criteria for the SCF cycle. As default
              a value of 1.d-7 is used.

     In the SCCDFTB program the atomtypes are represented by consecutive 
numbers. The definition of SCCDFTB atom numbers has to be accomplished 
before invoking the SCCDFTB command. The numbers are stored in WMAIN.
If the QM system e.g contains only O, N, C and H atoms,
the the numbering can be executed as follows:

scalar WMAIN set 1.0 sele type O*  SHOW end
scalar WMAIN set 2.0 sele type N*  SHOW end
scalar WMAIN set 3.0 sele type C*  SHOW end
scalar WMAIN set 4.0 sele type H*  SHOW end

Now, the O atoms are represented by 1.0, the N atoms by 2.0 etc. 

        Link atom may be added between an QM and MM atoms with the
following command:

ADDLinkatom  link-atom-name  QM-atom-spec  MM-atom-spec

      link-atom-name ::= a four character descriptor starting with QQ.

      atom-spec::= {residue-number atom-name}
                   { segid  resid atom-name }
                   { BYNUm  atom-number     }

        When using link atoms to break a bond between QM and MM
regions bond and angle parameters have to be added to parameter file
or better use READ PARAm APPEnd command.

        If define is used for selection of QM region put it after all
ADDLink commands so the numbers of atoms in the selections are not
changed. Link atoms are always selected as QM atoms.

File: SCCDFTB Node: Usage ]-[ Up: Top
Next: Installation -=- Previous: Description\n

SCCDFTB input files

SCCDFTB needs to read in the parameter files, which have 
a two-body character. Therefore, the interaction parmeters
for all pairs of atoms have to be read in.
These files are named like oo.spl, on.spl, oc.spl, no.spl etc.,
where oo.spl contains the two-center integrals for the O-O interaction,
on.spl the  two-center integrals for the O-N interaction etc.
DFTB needs these parameters for the O-N and N-O interaction,
similarily for all other pairwise interactions.
The file sccdftb.dat contains the paths to these parameters, as:

... \\
... \\
... \\

where atom-1 is the atom defined by 1.0, as described above,
atom-2 defined in WMAIN by 2.0 etc.

For the example of the system containing O N C and H, sccdftb.dat would


where PATH specifies the path to the directory where the data files 
are located. Be careful, an error in the sequence or a wrong assingnment
 of parameters to atoms (coordinates) will make results meaningless.
Parameter files can be requested from Marcus Elstner 

SCCDFTB output files (currently disabled)

SPE.DAT : contains the Kohn-Sham energies with occupations numbers.
CHR.DAT : contains the atomic  (Mulliken) charges of the atoms 
          (first row) and for the orbitals (s, px,py,pz,dxx.. ) in the 
          following columns.
REST.DAT: contains dipolemoment (D), calculated from the Mulliken 
          charges (not a reliable estimate of Dipolemoment in general!)

File: SCCDFTB Node: Installation ]-[ Up: Top
Next: Status -=- Previous: Usage\n

Installation of SCCDFTB

The source code of SCCDFTB ist distributed with CHARMM.
To compile the SCCDFTB method as the quantum part:
./install machine size T
T invokes the SCCDFTB 
The parameter files have to be reqeusted and stored in a directory,
which can be reached by 'PATH' (see up).

Diagonalization routines

As default, the library routine dsygv.f (LAPACK) is used for 
the diagonalization of the hamiltonian matrix.
This is called by chmdir/source/scctbint/scctbsrc/ewevge.f.
A faster (about factor 2) solution is given by the dsygvd.f routine 
(but less stable), which is called by ewevge-dsygvd.f: 
copy ewevge-dsygvd.f to ewevge.f and recompile to invoke this option.
Contact Marcus Elstner for more details or questions. 

File: SCCDFTB Node: Status ]-[ Up: Top
Next: Top -=- Previous: Installation\n

     The current implementation has analytical first derivative and thus
allows energy minimizations, reaction path search (e.g., travel) and
molecular dynamics simulations; SCC-DFTB/MM also works with Monte Carlo.
Replica can also be used, which makes it possible to use replica path
and related approaches (such the nudged elastic band) for determining
reaction path with the SCC-DFTB/MM potential; along the same line,
path integral simulations can be carried out as well, although only for
equilibrium properties at this stage.

     Several aspects of the code will be improved in the near future, and
new functionalities will be added:

1. Handling of QM/MM electrostatic interaction: currently no cut-off is
   used, which will be changed in the future. Ewald summation will 
   also be implemented.
2. Output from SCCDFTB (such as Mulliken charges) will be better 
3. Dispersion interactions among SCCDFTB atoms will be added.
4. Interface with centroid path-integral simulations and Tsallis
5. Interface with BLOCK for free energy simulations.
6. Unrestricted solution for open-shell systems.
7. Time-dependent treatment for electronically excited states.

CHARMM .doc Homepage

Information and HTML Formatting Courtesy of:

NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute