CHARMM c30b1 cheq.doc



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


                    The CHarge EQuilibration Method


The CHEQ and associated modules implement polarization via the
fluctuating charge method as based on the CHarge EQuilibration methods 
outlined in the literature.  While the current forcefield parameters are
valid for most small molecules and proteins, the force field is
constantly undergoing refinement and development.

The electrostatic model derives formally from the density functional
theory of atoms in molecules; polarization is effected as a result of
chemical potential equalization everywhere within a molecule, forcing
charge flow from regions of high to low chemical potential based on
atomic properties.  These properties are the atomic hardness and
electronegativity.  The parameters are treated as such and are
determined from fits to density functional calculations of charge
responses and mono- and dipole moments of small molecules in vacuum.

The method can be used to perform energy, minimization, and dynamics
calculations for the above-mentioned systems. For dynamics, the
charges are coupled to Nose-Hoover baths to maintain proper
adiabaticity.  Several normalization schemes are allowed to maintain
charge constant over desired partitions.  Several water models are
supported including the SPC-FQ and TIP4P-FQ models of Rick et al.

* Menu:

* Description::      Description of the CHEQ Function
* Syntax::           Syntax of the CHEQ commands
* Options::          CHEQ Command Options
* Energy::           Usage with Energy and Dynamics commands
* Scalar::           Usage with the Scalar Command
* Examples::         Usage Example Script
* References::       References for CHEQ Methods



File: CHEQ ]-[ Node: Description
Up: Top -=- Previous: Top -=- Next:Syntax\n

The CHarge EQuilibration routines implement the fluctuating charge
dynamics as described in recent literature (1-9).  The method derives
from the density functional theory of atoms in molecules.  The model
is a relatively simple approach to incorporate a means for electronic
density rearrangement (as reflected grossly in terms of some
partitioned 'charge' on an atom) due  to changes in chemical
environment---polarizability.  The mechanism for the redistribution is
the equalization of electronic chemical potential everywhere within a
molecule, a statement of Sanderson's principle of electronegativity
equalization ( since, in DFT, the chemical potential and
electronegativity  are analogous).  The electrostatic potential
adopted in this formalism is (for a system with M molecules with N_i
atoms in molecule 'i':
                                          __                       __
                                         /                           \
     N  N_i                       M   M  |  N   N                     |
E = sum sum CHI_ia(0) Q_ia + 1/2 sum sum | sum sum ETA_iajb Q_ia Q_jb |
    i=1 a=1                      i=1 j=1 | a=1 b=1                    |
                                         \__                       __/
     

The ETA_iajb term comes from the hardness matrix whose elements are
determined  via (Ref. 13): 

                             1/2 ( ETA_i + ETA_j)
        ETA_ij = ---------------------------------------------
                  sqrt( 1 + 0.25 (ETA_i + ETA_j)**2 R_ij**2)

Atoms involved in bonded interactions, angle interactions, and
dihedral interactions interact with each other via the combination
rule.  Atoms in a molecule separated by more than three bonds interact
with the normal Coulomb 1/R interaction, as do charge sites on
different molecules.

The model requires parameterization of atomic electronegativities and
hardnesses.  The hardness are determined via fitting the DFT charge
responses of small molecules containing the chemical functional groups
of interest in modelling proteins.  The approach is hierarchical,
beginning with the fitting of aliphatic groups (methyl carbons,
hydrogens, for instance), and then carrying these over into the
determination of other groups.  The electronegativities then are
determined by fitting to charge distributions and dipole moments of
isolated small molecules in vacuum.

A fictitious charge dynamics is performed in the spirit of
Car-Parrinello or 'ab initio' molecular dynamics simulations. The
charge sites are given masses (much smaller than the nuclei so as to
maintain the system on the Born-Oppenheimer (BO) surface) and the
entire system is propagated with an extened Lagrangian which enforces
the required charge normalization.  The charges are thermostatted to
heat baths to maintain a relatively low temperature to ensure
adiabaticity.  Currently this is done via coupling to Nose-Hoover heat
baths; groupings of charges can be separately coupled so as to avoid
'hot spots'.



File: CHEQ ]-[ Node: Syntax
Up: Top -=- Previous: Description -=- Next: Options\n

                         Syntax of the CHEQ commands

CHEQ [ON   ]
     [OFF  ]
     [RESEt]

     [NORM ] {BYRE | BYAL | BYSE | BYGP | BYMO} atom_selection

     [QMAS ] CGMA {charge-mass}  TSTA {initial temperature} atom_selection

     [TIP4p] atom_selection
     [WATEr]
     [SPC  ]
     [FLEX ]

      CHEQ {WATE | SPC | FLEX} SELECT {selection} END




File: CHEQ ]-[ Node: Options
Up: Top -=- Previous: Syntax -=- Next: Energy\n


                            CHEQ Command Options


ON    sets QCG flag to .TRUE. (turns on fluctuating charges). This can
      be issued anytime in order to switch between non-polarizable and
      polarizable Hamiltonians

OFF   sets QCG flag to .FALSE. (turns off fluctuating charges). This
      can be issued anytime in order to switch between non-polarizable
      and polarizable Hamiltonians.

RESE  turns off CHEQ (QCG=.FALSE.) and resets some CHEQ arrays and 
      parameters as follows:

      The variable 'QNPART' is set to zero (nullifies CHEQ
      normalization units; the user will have to respecify these with
      'CHEQ NORM norm-option atom-selection as discussed under the
      'NORM' option command. 

      QCG is set to FALSE; thus, ENERGY, MINIMIZATION, and DYNAMICS
      using the CHEQ method is no longer possible unless the CHEQ
      option us used with the relevant commands.

      All arrays associated with the partitions, partition counters,
      and pointers to atoms of partitions are zeroed.

NORM  sets up partitions for charge normalization.  Implemented by 
      setting total charge force for a partition to zero.  Format for 
      command:
      CHEQ NORM {BYRE | BYAL | BYSE | BYGP | BYMO} SELECT {selection} END
      description of options:
      BYRE - charge constant within residues in the given selection
      BYAL - charge constant within all atoms in the given selection
      BYSE - charge constant within segments in the given selection
      BYGR - charge constant within groups in the given selection
      BYMO - charge constant within molecules in the given selection
      NOFQ - turns off CHEQ for selected atoms


QMAS  sets up mass and initial temperature for charges

      QMAS CGMA {charge-mass}  TSTA {initial temperature} {atom selection}


TIP4  selects the TIP4P-FQ water model of Rick and Berne
      Note: Consult the LONEPAIR documentation for properly setting up the 
            constructs necessary to implement this 4-point water model and/or 
            check the testcases

WATE  Rigid water, derivatives of intra-molecular hardness elements with
      respect to coordinates are not computed.

SPC   selects rigid 3-point water using special SPC parameters of Rick and Berne

FLEX  generic CHEQ molecule type (flexible molecule; charge force on
      nuclei computed).  The above options (WATE, SPC and FLEX, TIP4)
      are used similarly to the NORM command:

      CHEQ {WATE | SPC | FLEX} SELECT {selection} END

PRIN  Prints out several variables and arrays for CHEQ

WALP  sets parameters for restraint potential to bound charges on
      atoms; this is to prevent over-polarization in cases where the
      charges sample regions further away from the minimum determined
      by the quadratic form of the CHEQ potential.  At this time, only
      two forms of the restraint are supported.  Can be extended in
      the future. 

      For PTYP = 1 :

      CHEQ WALP { PTYP integer} { QRQ1 real } { QRQ2 real } { QRK real } -
           atom_selection

      For PTYP = 2 :

      CHEQ WALP { PTYP integer} { WALN integer } -
           { QRA1 real } { QRAB1 real } { QRA2 real } { QRB2 real } -
           { QRQ1 real } { QRQ2 real } { QRK real } atom_selection

      PTYP sets the type of restraint potential; 1=harmonic, 2=Nth
      order wall potential with switch. (Ref #)

      QRQ1 the upper limit of the values a certain charge can take
      QRQ2 the lower limit of the values a certain charge can take
      QRK  the force constant for harmonic restraint or the strength
           for the wall potential (generally on the order of 10**2)
  
      The following are further specifications needed for a
      non-harmonic wall potential. 

      WALN  integer value setting the hardness of the wall potential
      QRA1  charge value below which switching function is zero 
      QRB1  charge value above which switching function is unity
      ** QRA1 < QRB1

      QRA2  charge value above which switching function is zero
      QRB2  charge value below which switching function is unity
      ** QRA2 < QRB2




File: CHEQ ]-[ Node: Energy
Up: Top -=- Previous: Options -=- Next: Scalar\n


                        Energy and Dynamics


CHEQ can be used with ENERgy, MINImization, and DYNAmics commands.
Currently, minimization routines supporting CHEQ are the CONJugate
gradients and STEEPest descents.  For DYNAmics, the leapfrog
integrator includes charge dymamics.
        
For these functions, the CHEQ flag must be specified so that the
appropriate subroutines are used:

     ENERGY energy_options  CHEQ CHEQ_options

     DYNA dynamics_options  CHEQ CHEQ_options

     MINI minimization_options  CHEQ CHEQ_options

where CHEQ_options are as in the following.

NOCO  sets QNOCO flag to .TRUE.  Freezes coordinates by zeroing DX,DY and DZ
      resets to .FALSE. when exiting ENERgy, MINImization, or DYNAmics call.
      Useful for minimizing charge for a fixed conformation.  For a large 
      system this can be faster than CGIN since the charges tend to converge
      rapidly.(<100 steps for 216 water system)

CGMD  Used with ENERgy, MINIimization, and DYNAmics calls
 
      int - 0 for normal Hamiltonian with exclusion in  elec.interactions
              (default) 
            1 using Hamiltonian without exclusions (Recommended for FLUQ)

CGIN  Used with ENERgy call
 
      charges will be calculated by matrix inversion whenever energy is
      called. (WARNING: it is slow and memory intensive on big systems)
      This option does not work with IMAGES.(but does work with BOUND)
      This keyword must be specified every time it is wanted as the flag
      CGINV is set to .FALSE. after the command is performed.


POLT  Used with ENERgy call

      calculates the components of the molecular polarizability tensor
      based on the molecular geometry and hardness matrix
      elements. Used in conjunction with the ENERGY call.

      Use care when comparing to experimental data; usually need to
      make sure that the same molecular orientations are being
      compared (i.e, planar water case, depending on the orientation,
      will get different results for the tensor component values).
   
FQPA  Prints out the Eta matrix when doing matrix inversion. (i.e. only works 
      in conjunction with CGIN keyword)  This is an NATOM by NATOM array so can 
      get very large.  Flag resets to .FALSE. after command has executed.


FQINT  used with DYNAmics call

       sets the charge integration algorithm
       1 = Nose-Hoover Temperature Control **
       2 = No temperature control
       required as input; default does not do charge dynamics 

    ** Note: To use the Nose-Hoover algorithm for propagating the
       charge dynamics with temperature control, one must specify the
       degrees of freedom which are to be coupled to a given bath.
       The method for specifying this is similar to the multi-heat
       bath calls for the NOSE command to thermostat the nuclear
       degrees of freedom.  The following command must be issued
       before the call to DYNAMICS: 

           FQBA  I            
           CALL J  atom-selection-option
           COEF J  QREF (0.005) TREF (1.0)
           .
           .
           .
           . 
           END

       The integer 'I' indicates the number of baths for groupings of
       charge degrees of freedom.  For each bath, the 'CALL' and
       'COEF' commands set the atoms coupled to that bath, the
       Nose-Hoover fictitious mass, QREF, for that bath, and the
       temperature, TREF, for that bath.

    ** CHEQ computation now turns on and off with SKIPE command.  Tied
      to ELEC keyword. If SKIPE ELEC command is given CHEQ energy and
      derivatives are set to zero.
       



File: CHEQ ]-[ Node: Scalar
Up: Top -=- Previous: Energy -=- Next: Example\n


                            SCALAR Command


The charge array has always been available from the scalar command, but 
there are now additional arrays specific to Fluc-Q that are accessible, 
namely the charge derivatives as well as both the eta and chi parameters.
The keynames that have been added are:

    DCH  - charge derivatives
    EHA  - hardness parameters for every atom
    ECH  - electronegativity parameters for every atom

See the description of the * scalar command: (scalar.doc). for useage.

For information regarding variables used in conjunction with the CHEQ method,
consult the include files cheqdyn.fcm and derivq.fcm in the source/fcm
diretory.



File: CHEQ ]-[ Node: Example
Up: Top -=- Previous: Scalar -=- Next: References\n


                                Examples


There are examples of many of the commands described above in the test
input script that is in the test/c30test directory.  After the
structure has been generated the CHEQ options can be set up.
A typical sequence of commands might go something like:

{read RTF}                  ! read appropriate file to obtain CHEQ parameters;
                            ! treated analogous to charges
{read standard parameters}

{read sequence}
GENErate

CHEQ norm byre select all end      ! normalization over residues
CHEQ flex select all end           ! Flexible molecules 

energy cheq cgmd 1



File: CHEQ ]-[ Node: References
Up: Top -=- Previous: Examples -=- Next: Top\n


                                References


1.  Parr, R. G., and W. Yang. Density-Functional Theory of Atoms and
    Molecules. 1989. Oxford: Oxford University Press.

2.  Sanderson, R. T. "Chemical Bonds and Bond Energy". 2nd. Edition,
    1976, New York, Academic. 

3.  Sanderson, R. T. Science. 114. 1951, p.670.

4.  Rick, S. W., S. J. Stuart, B. J. Berne. J. Chem. Phys. 101(7).
    1994 pp.6141-6156.

5.  Rick, S. W. and B. J. Berne.  JACS. 118, 1996. pp672-679.

6.  Mortier, W. J., S. K. Ghosh, S. Shankar. JACS. 108, 1986. pp.4315-4320.

7.  Mortier, W. J., K. V. Genechten, and J. Gasteiger. JACS. 107,
    1985. pp.829-835. 

8.  Rappe, A. K. and W. A. Goddard, III. J. Phys. Chem. 95, 1991. pp.3358-3363. 

9.  York, D. M. and W. Yang. J. Chem. Phys. 104(1), 1996. p.159.

10. Car. R, and M. Parrinello. Phys. Rev. Lett. 55, 1985. p.2471.

11. Blochl, P. E., and M. Parrinello. Phys. Rev. B. 45(16), 1992. p.9413.

12. Yoshii, N., R. Miyauchi, S. Miura, S. Okazaki. Chem. Phys. Lett. 317,
    2000. pp.414-420.

13. Naleewajski, R. F., J. Korchowiec, and Z. Zhou. Int. J. Quant. Chem. 
    Quantum Chemistry Symposium 22, 1988. pp.349-366.

----------------------------------------------------------------------
   
  <Known Incompatible with (so far)> 
   - FASTEW (SGI and GNU PME performance optimizations)


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