CHARMM c30b1 pbeq.doc



File: PBEQ ]-[ Node: Top
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                 Poisson-Bolztmann Equation Module   

    The PBEQ module allows the setting up and the numerical solution of
the Poisson-Boltzmann equation on a discretized grid for a solute molecule.

Attention: Problems should be reported to
         . Benoit Roux    at Benoit.Roux@med.cornell.edu, phone (212) 746-6018
         . Wonpil Im      at Wonpil.Im@cornell.edu
         . Dmitrii Beglov at beglovd@moldyn.com

* Menu:

* Syntax::      Syntax of the PBEQ commands
* Function::    Purpose of each of the commands
* Examples::    Usage examples of the PBEQ module



File: PBEQ ]-[ Node: Syntax
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                                 Syntax

[SYNTAX PBEQ functions]

Syntax:

PBEQ          enter the PBEQ module
END           exit the PBEQ module

Subcommands:

SOLVe          PB-theory-specifications
               solver-specifications         grid-specifications
               iteration-specifications      charge interpolation-spec.
               boundary potential-spec.      dielectric boundary-spec.
               physical variable-spec.       membrane-specifications
               spherical droplet-spec.       orthorhombic box-spec.
               cylinder-specifications       solvation force-spec.
               atoms-selection

ITERate        PB-theory-specifications      solver-specifications         
               iteration-specifications 

ENPB           [INTE  atoms-selection] 

CAPAcitance 

COUNTERION

WRITE          property [[CARD] [write-range]] [UNIT  integer]

READ           [PHI] [PHIX] [FKAP] [MIJ] [UNIT  integer]

COOR           coordinate-manipulation-command

SCALar         scalar-manipulation-command

PBAVerage      [PHI] [ATOM atom-selection] [UPDATE] [units]
               grid-specifications

HELP 

RESET

PB-theory-specifications::= [NONLinear] [PARTlinear] 
default             : linear PB by default (no need to specify)
NONLin	[.FALSE.]   : non-linear PBEQ solver
PARTlin	[.FALSE.]   : partially linearized PBEQ solver

solver-specifications::=[OLDPB] 
[OSOR] [UNDER] [[FMGR] [NCYC integer] [NPRE integer] [NPOS integer]]
default             : SOR (Successive OverRelaxation) method for linearized PB
OLDPB	[.FALSE.]   : old PBEQ solver (used in c26a2)
OSOR	[.FALSE.]   : optimization of the over-relaxation parameter
UNDER	[.FALSE.]   : Under-relaxation for non-linear and partially linearized
                      PBEQ solvers with fixed LAMBda value
FMGR	[.FALSE.]   : full multigrid method
NCYC	[100]       : maximum number of cycles (in FMGR)
NPRE	[2]         : number of relaxation for PRE-smoothing (in FMGR)
NPOS	[2]         : number of relaxation for POST-smoothing (in FMGR)

grid-specifications::= [NCEL integer] [DCEL real] 
                       [NCLX integer] [NCLY integer] [NCLZ integer] 
                       [XBCEN real]   [YBCEN real]   [ZBCEN real]
NCEL	[65]        : number of grid point in 1D for a cubic
DCEL	[0.1]       : size of grid unit cell
NCLX    [NCEL]      : number of grid point in X for general parallelepiped
NCLY    [NCEL]      : number of grid point in Y for general parallelepiped
NCLZ    [NCEL]      : number of grid point in Z for general parallelepiped
XBCEN   [0.0]       : the center of a box in X
YBCEN   [0.0]       : the center of a box in Y
ZBCEN   [0.0]       : the center of a box in Z

iteration-specifications::=[MAXIter integer] [DEPS real] 
                           [DOMEga real]     [LAMBda real]  [KEEPphi]
MAXIter	[2000]	    : number of iterations
DEPS	[0.000002]  : parameter (tolerance) of convergence 
DOMEga	[1.0]       : initial mixing factor
LAMBda	[1.0]       : initial mixing factor (LAMBda = DOMEga)
KEEPphi	[.FALSE.]   : Use the potential from previous calculation
                      as a initial guess for current calculation

charge interpolation-spec.::= [BSPLine]
default             : the trilinear interpolation method
BSPLine [.FALSE.]   : the Cardinal B-spline method is used?

boundary potential-specifications::= [ZERO] [INTBP] [FOCUS] [PBC] [NPBC]
                                     [NIMGB integer] 
default             : use the Debye-Huckel approximation at each boundary point
                      use XY periodic boundary conditions in membrane
                      calculation 
INTBP   [.FALSE.]   : INTerpolation of Boundary Potential is used?
ZERO    [.FALSE.]   : boundary potential is set to ZERO ?
                      (metallic conductor boundary conditions)
FOCUS   [.FALSE.]   : previous potential is used to set up boundary potential?
PBC	[.FALSE.]   : 3d periodic boundary condition
NPBC	[.FALSE.]   : supress XY periodic boundary conditions in membrane
                      calculations
NIMGB	[0]         : use the image atoms for boundary potential 
                      in membrane calculation 
                     (NIMGB=1 means the 8 nearest image cells)
                     (NIMGB=2 means the 24 nearest image cells, i.e.,
                      2 shells of images)

dielectric boundary-specifications::= [SMOOTH] [SWIN real] [REEN]
default             : the vdW surface is used for the dielectric boundary
SMOOth	[.FALSE.]   : invoke smoothing dielectric boundary
SWIN	[0.5]       : solute-solvent dielectric boundary Smoothing WINdow
REEN	[.FALSE.]   : the molecular (contact+reentrant) surface is created 
                      with WATRadius for the dielectric boundary

physical variable-specifications::= [EPSW real] [EPSP real] 
                                    [WATR real] [IONR real] 
                                    [CONC real] [TEMP real] 
EPSW	[80.0]      : bulk solvent dielectric constant
EPSP	[1.0]       : protein interior dielectric constant
WATR	[0.0]       : solvent probe radius
IONR	[0.0]       : ion exclusion radius (Stern layer)
CONC	[0.0]       : salt concentration [moles/liter]
TEMP	[300.0]     : Temperature [K]

membrane-specifications:: [TMEMb real] [HTMEmb real] [ZMEMb real] [EPSM	real]
                          [EPSH	real]  [VMEMB real]
TMEMB	[0.0]	    : thickness of membrane (along Z) 
HTMEMB	[0.0]	    : thickness of headgroup region
ZMEMB	[0.0]	    : membrane position  (along Z)
EPSM	[1.0]	    : membrane dielectric constant
EPSH	[EPSM]	    : membrane headgroup dielectric constant (optional)
VMEMB	[0.0]	    : potential difference across membrane (entered in [volts])

spherical droplet-spec.::= [DROPlet real]  [EPSD real]
                           [XDROplet real] [YDROplet real] [ZDROplet real]
                           [DTOM] [DKAP]
DROPlet	[0.0]      : radius of spherical droplet
EPSD   	[1.0]      : dielectric constant of spherical droplet
XDROp	[0.0]      : position of spherical droplet in X
YDROp	[0.0]      : position of spherical droplet in Y
ZDROp	[0.0]      : position of spherical droplet in Z
DTOM	[.FALSE.]  : the dielectric constant of the overlapped region 
                     with membrane is set to EPSM ?
DKAP	[.FALSE.]  : the Debye-Huckel factor inside sphere is set to KAPPA ?

orthorhombic box-spec.::= [LXMAx real] [LYMAx real] [LZMAx real] 
                          [LXMIn real] [LYMIn real] [LZMIn real] 
                          [BTOM]       [BKAP]
LXMAx	[0.0]       : maximum position of a box along X-axis
LYMAx	[0.0]       : maximum position of a box along Y-axis
LZMAx	[0.0]       : maximum position of a box along Z-axis
LXMIn	[0.0]       : minimum position of a box along X-axis
LYMIn	[0.0]       : minimum position of a box along Y-axis
LZMIn	[0.0]       : minimum position of a box along Z-axis
EPSB    [1.0]       : dielectric constant inside box
BTOM	[.FALSE.]   : the dielectric constant of the overlapped region 
                      with membrane is set to EPSM ?
BKAP	[.FALSE.]   : the Debye-Huckel factor inside box is set to KAPPA?

cylinder-specifications::= [RCYLN real] [HCYLN real] [EPSC real]
                           [XCYLN real] [YCYLN real] [ZCYLN real]
                           [CTOM]       [CKAP]
RCYLN	[0.0]       : radius of cylinder
HCYLN	[0.0]       : height of cylinder
EPSC	[1.0]       : dielectric constant inside cylinder
XCYLN	[0.0]       : position of cylinder in X
YCYLN	[0.0]       : position of cylinder in Y
ZCYLN	[0.0]       : position of cylinder in Z
CTOM	[.FALSE.]   : the dielectric constant of the overlapped region 
                      with membrane is set to EPSM ?
CKAP	[.FALSE.]   : the Debye-Huckel factor inside cylinder is set to KAPPA?

solvation force-spec.::= [FORCE] [STEN real] [NPBEQ integer]
FORCe	[.FALSE.]   : invoke solvation force calculation
STEN	[0.0]       : surface tension coefficient (in kcal/mol/A^2)
NPBEQ   [1]	    : the frequency for calculating solvation forces 
                      during minimizations and MD simulations

write-range::= [XFIRST real] [YFIRST real] [ZFIRST real]
               [XLAST  real] [YLAST  real] [ZLAST  real]
 
property::=  [[PHI] [KCAL] [VOLTS]]    [[PHIX] [KCAL] [VOLTS]]
             [FKAPPA2]
             [CHRG]
             [EPSX] [EPSY] [EPSZ]
             [MIJ]
             [TITLE]
PHI     : electrostatic potential [ KCAL/MOL ] [ VOLTS ]
          (default  [UNIT CHARGE]/[ANGS])
PHIX    : external static electrostatic Potential [ KCAL/MOL ] [ VOLTS ]
          (default  [UNIT CHARGE]/[ANGS])
FKAPPA2 : Debye screening factor
CHRG    : charges on the lattice
EPSX    : X sets of dielectric constant
EPSY    : Y sets of dielectric constant
EPSZ    : Z sets of dielectric constant
MIJ     : MIJ matrix
TITLE   : formatted title line

atoms-selection::= a selection of a group of atoms 




File: PBEQ ]-[ Node: Function
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        General discussion regarding the PBEQ module

1.  SOLVE 
    Prepare grids and solve PB equation for the selected atoms and return the 
electrostatic free energy in ?enpb = (1/2)*Sum Q_i PHI_i over the lattice.
The factor of 1/2 is there for the linear response free energy of charging.
The atomic contributions are returned in WMAIN (destroying the radii).  

NOTE: At the first stage of PBEQ or after "RESET", WMAIN should be set to 
      the atomic radii for the calculation.  After a call to SOLVE the atomic
      radii are saved in a special array.  The atomic contribution to the 
      electrostatic free energy are returned in WMAIN (destroying the radii).
      To modify the value of the radii, the keyword RESET must be issued.

  1) PB SOLVERs 
     (Reference: Klapper et al.  Proteins 1, 47 (1986)
                 A. Nicholls et al; J. Comput. Chem, 12(4),435-445 (1991))
     Currently, PBEQ module supports various PB equation solvers. 
     The default solver uses the SOR (Successive OverRelaxation) method for 
     the linearized PB equation.  
     This is much faster than the old PBEQ solver which was used in c26a2.
     With OSOR keyword, the relaxation parameter will be optimized.  This is
     especially useful when the system contains a salt concentration.
     Solvers for non-linear and partially linearized PB equations for
     1:1 charge-paired salt are now available. Both use the SOR method as a 
     default. In many cases, the direct use of both solvers may cause some 
     convergence problems. So, it is the best way to use the potential from 
     the linearized PB equation as a initial guess. Though, you may want to 
     use the under-relaxation by adjusting the mixing factor (LAMBda).  
     The partially linearized PB equation means that the linearized form of
     one of two exponential function is used like
              phi > 0 --> exp(phi)  = 1 + phi
              phi < 0 --> exp(-phi) = 1 - phi
     Full multigrid (FMG) method is efficient for the uniform dielectric
     medium.  When there is a discontinuity in the dielectric function,
     the method could be slower than the SOR method.  You can improve the
     calculation speed using the smoothing dielectric boundary.  Cubic grid
     should be used and number of grid points should be 2**(n+1) where n is
     a integer upto 9.  Currently, FMG does not support MEMBRANE and PBC.
     (see ~chmtest/c28/pbeqtest5.inp and pbeqtest6.inp)

  2) Grid
     The number of grid points in X, Y, and Z (NCEL,NCLX,NCLY,NCLZ) must
     be odd.  Otherwise, the number of grid points will be increased by ONE
     without any WARNING message.

  3) Iteration
     The maximum number of iterations (MAXIter) can be specified.  
     The convergence parameters DEPS should not be modified.
     One could use the potential from previous calculation as a initial 
     guess for current calculation using KEEPphi keyword.  This is useful for
     the nonlinear (or partially linearized) PB equation.  See also ITERate.

  4) Charge Distribution Method
     The default is the trilinear method to distribute a charge over
     nearest 8 grid points. BSPLINE keyword will invoke the 3rd-order 
     B-splines interpolation over nearest 27 grid points. 
     B-splines method removes discontinuities in the reaction field forces.

  5) Boundary Potential
     By default, boundary potential is calculated using the Debye-Huckel
     approximation for every boundary point.  However, the computational 
     time increases prohibitively as the number of grid points and of atoms 
     in the system increases.
     INTBP keyword uses the bilinear interpolation to construct
     boundary potential in a box with DCEL and (NCLx,NCLy,NCLz) from those 
     in the same box with 2*DCEL and (NCLx/2+1,NCLy/2+1,NCLz/2+1).  
     ZERO keyword sets boundary potential at the edge of the grid to zero.
     FOCUS keyword uses previously calculated potentials to set up boundary 
     potential. 
     (Reference: M.K. Gilson et al; J. Comput. Chem. 9(4),327-335 (1987)) 
     (see also an example below)
     PBC keyword invokes the full 3d periodic boundary condition so that
     no boundary potential is calculated directly using the Debye-Huckel
     approximation.
     (Reference: P.H. Hunenberger and J.A. McCammon JCP v.110(4) p.1856 (1999))
     (alos, see ~chmtest/c28/pbeqtest4.inp)
     NPBC keyword surpress XY periodic boundary conditions in membrane 
     calculations.
     Boundary potential of XY plane in membrane calculations can be constructed
     using the image atoms. When NIMGB=1, boundary potential includes the 
     influence of the 8 nearest image cells.    


  6) Dielectric boundary
     SMOOTH and REEN change the attribute of the solute-solvent boundary.  
     By default (NO SMOOTH), the boundary is defined by the van der Waals 
     surface or the molecular surface (with WATR).  SMOOTH keyword changes 
     the boundary as a region having +/- SWIN (Smoothing WINdow) from the 
     surface of the solute.  Within the solute-solvent boundary, 
     the dielectric constant and the Debye screening factor will be changed 
     continuously from EPSP and zero to EPSW and the screening factor 
     at bulk solvent.
     REEN keyword with WATR creates the molecular (contact+reentrant) surface
     as the dielectric boundary.
     
     NOTE: WATR without REEN just increases the atomic radii by it.   

  7) Various geometric objects
     PBEQ module supports three geometric objects with various options
     (see spherical droplet-, orthorhombic box-, and cylinder-spec. above)
     When using more than one geometry at the same time, the order of creating
     geometries is as follows: first is a droplet, second is a cylinder, and 
     the last is a box.

  4) Solvation force
     This keyword invokes the calculation of the solvation free energy and 
     forces and must be followed by SMOOTH keyword.  The solvation energy is
     taken as a sum of electrostatic and nonpolar solvation energy.  
     The former is calculated from the PB equation and the latter by using 
     the surface tension coefficient (STEN) that relates free energy with 
     surface area.  Note that the calculated surface is approximately the 
     van der Waals surface.  If membrane is considered, the surface of the 
     membrane is also approximately included. The corresponding forces are 
     also calculated and will be used in minimizations and MD simulations 
     where NPBEQ can be used to specify the frequency for calculating the 
     solvation forces.  Note that SWIN must be equal or greater to DCEL to 
     get correct solvation free energy and forces. 
     (Reference: W. Im, D. Beglov and B. Roux 
                 Continuum Solvation Model: computation of electrostatic
                 forces from numerical solutions to the PB equation,
                 Comput. Phys. Commun. 109,1-17 (1998))
     NOTE:To print out the force of each atom, PRNLEV should be greater
          than 6.

2.  ITERATE 
    Pursue the iteration on the grid. SOLVE must have been called first.
    The main difference with the keyword KEEPphi (see above) is that the
    physical specifications (e.g., dielectric interface, membrane, etc...)
    must remain the same with ITERate.  However, it is possible to change 
    from linear to non-linear PB using ITERate. (see pbeqtest5.inp)

3.  ENPB    
    Compute the electrostatic PB energy Sum Q_i PHI_i over the lattice.
Notice that the electrostatic energy is twice as much as the electrostatic
free energy (see above).  The value of the electrostatic energy is passed
through the substitution parameter enpb.  With INTE keyword, you can specify
the atoms of interest.

4.  CAPACITANCE
    Compute the capacitance based on the net induced charge in the double 
layer.  The induced charge beyond the limits of the box are estimated based on
the analytical solution to a planar membrane.

5.  COUNTERION
    Compute the counter-ion (1:1 salt) distribution along Z-axis.

6.  WRITE
    The WRITE command is used to write out the grid properties.  By default, 
a binary file of the property will be written for the whole grid.  The keyword 
CARD implies that a formatted output will be produced.  In that case, the 
spatial range can be specified for the output.  By default, the electrostatic 
potential PHI is given in [UNIT CHARGE]/[ANGS].  If specified, the PHI can be 
given in [VOLTS] or in [KCAL/MOL].

7.  READ
    The READ command is used to read the electrostatic potential PHI or PHIX
    in [UNIT CHARGE]/[ANGS], Debye screening factor FKAPPA2, and 
    the generalized reaction field MIJ matrix written in a binary file.

8.  RESET
    Resets all assignments of the PBEQ module and free the HEAP array.  
Destroys all lists and grids.  By default, the grids and arrays remain assigned
when exiting and re-entering the PBEQ module.  This is to allow multiple call 
to PBEQ without having to free the HEAP and other arrays if they are going 
to be used again. The RESET keyword must be used to re-assign new values for
the atomic radii.  

9.  Miscellaneous command manipulations
*note misc: (miscom.doc) are supported within the PBEQ module,
allowing opening and closing of files, streaming of files, label assignments
(e.g., LABEL), and repeated loops (e.g., GOTO), parameter substitutions
(e.g., @1,@2, etc...) control (e.g., IF 1 eq 10.0 GOTO LOOP) and CALC
(e.g., CALC energy = ?enpb).

NOTE: TIMER 2 gives the times of various components in PBEQ module;
      the grid parameter preparation (subroutine MAYER),
      iterative solution (subroutine PBEQ1), and,
      force calculation (subroutine RFORCE and BFORCE).

10.  COORMAN and SCALAR commands 
*note misc: (corman.doc) and (scalar.doc) are supported within 
the PBEQ module, allowing the easy manipulation of charges, radii, rotation
and translations of molecules, etc...

11. A set of "ATOMIC BORN RADII"
    Atomic radii derived from solvent electrostatic charge distribution may be 
used. (test/data/radius.str) These radii were tested with free energy 
perturbation with explicit solvent. 
(Reference: M. Nina, D. Beglov and B. Roux.
            Atomic Radii for Continuum Electrostatics Calculations based on 
            Molecular Dynamics Free Energy Simulations. 
            J. Phys. Chem. 101(26),5239-5248,1997).

NOTE:  A typo for residue HSD was present in the original set of radii.
       Check with M. Nina for new updated file.
 
To get the set of appropriate radii when using SWIN, 
the commands are as follows;

        STREAM RADIUS.STR
        SCALAR WMAIN ADD {SWIN}
        SCALAR WMAIN MULT {FACTOR}
        SCALAR WMAIN SET 0.0 SELE TYPE H* END

The factor has a linear relationship with SWIN.
-----------------------------------------------------------------------------
SWIN    0.1   0.2    0.3    0.4    0.5    0.6    0.7    0.8    0.9    1.0
FACTOR  0.979 0.965  0.952  0.939  0.927  0.914  0.901  0.888  0.875  0.861
-----------------------------------------------------------------------------
** FACTOR = -0.1296 x SWIN + 0.9914 (a least-square fit)

12.  PBAVerage subcommand

This subcommand allows for the averaging of the (precalculated) electrostatic
potential (PHI values) over specified regions of the grid.  The region is 
specified as a rectangular box, with or without an atom selection.  The units
may be specified as KCAL (kcal/mol), VOLT (volts), or not at all, in which 
case the default units (charge/angs) are used.  The calculated average may
be assigned to a CHARMM parameter through the symbol ?AVPH.  The PBAV PHI
subcommand does not calculate the PHI values themselves; hence the electro-
static potential should have already been calculated before this subcommand
is given.

The following calculates the average PHI value over a rectangular-box region
of the grid:

PBAV PHI KCAL xfirst [real] xlast [real] -
              yfirst [real] ylast [real] -
	      zfirst [real] zlast [real]

The grid limits must be specified the first time the PBAV PHI subcommand is
invoked.  For subsequent invocations, the command will use the stored limits
unless the limits are respecified.

The following calculates the average PHI values over the grid points that are 
both within the grid limits and within the van der Waals radii of the selected
atoms:

PBAV PHI KCAL UPDAte xfirst [real] xlast [real] -
                     yfirst [real] ylast [real] -
                     zfirst [real] zlast [real] -
ATOM SELE [selection] END

The UPDAte keyword updates the atom-based grid, so that when the
PBAV PHI ATOM subcommand is given for the first time, the UPDATE keyword
must be used and an atom selection given.  For subsequent invocations, 
the atom selection (for defining the set of atoms over which the
calculation is to be done) and the UPDATE command (for updating the
grid, based on the position of the selected atoms) are optional.
If UPDATE is specified but the atom selection (or grid limits) are not,
the algorithm will use the atom selection (or grid limits) that were 
last specified.  If the PBAV PHI subcommand has not been
previously given, the grid limits must be specified.



File: PBEQ ]-[ Node: GSBP
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              Generalized Solvent Boundary Potential (GSBP)

    GSBP is a boundary potential for simulating a reduced system while 
incorporating implicitly the dominant electrostatic forces of the surrounding
atoms.  It has been developed in the same spirit as the SBOUND and the SSBP,
see *note sbound:(sbound.doc) and ssbp:(mmfp.doc).  

The current implementation of the method is described in W. IM, S. Berneche, 
and B. Roux. J. Chem. Phys. (2000, in preparation).  Briefly, the system is
partitioned in two regions: an inner region of interest and an outer region.
The inner region includes all atom explicitly.  

GSBP represents the electrostatic forces from the outer region as the sum of 
two components.  One is the static external field (PHIX) which arises from 
the charge distribution in the outer region (taking into consideration the
solvent as a featureless dielectric medium). The second contribution is
the reaction field which is created by the charge distribution inside the
inner region considering the whole molecular configuration and the dielectric
solvent.  In the GSBP, the reaction field is calculated through a generalized
multipolar expansion of the instantaneous charge density in the inner system
coupled with a generalized reaction field matrix MIJ. 

    The numerical implementation of the GSBP can be divided into two parts;  
SETUP and UPDATE parts. In the SETUP part,  the static external field and the 
MIJ matrix are calculated once and stored before a simulation. The SETUP part
mostly uses the PBEQ module.  In UPDATE part, the energy and forces are 
updated using the stored external field and the MIJ matrix in each step of 
the molecular dynamics.

1. GSBP Syntax
   GSBP is a subcommand inside PBEQ module like SOLVe and uses all options 
(except solvation force-spec.) in SOLVe.


   GSBP           decomposition-spec.           inner region-specifications 
                  basis functions-spec.         large box-specifications
                  all options in SOLVE

   decomposition-spec.::= [GTOT] [G_oo] [G_io] [G_ii] 
   GTOT      [.FALSE.]   : total electrostatic solvation free energy
   G_oo      [.FALSE.]   : electrostatic solvation free energy in outer region
   G_io      [.FALSE.]   : electrostatic free energy due to the interactions
                           between inner and outer regions
   G_ii      [.FALSE.]   : electrostatic solvation free energy in inner region

   inner region-specifications:: [ [RECTbox] 
                                   [XMAX real]  [YMAX real]  [YMAX real]  
                                   [XMIN real]  [YMIN real]  [YMIN real] ] 
                                 [ [SPHEre]
                                   [SRDIst real]
                                   [RRXCen real] [RRYCen real] [RRZCen real] ]
   RECTbox   [.FALSE.]   : rectangular (box) inner region
   XMAX	     [0.0]       : maximum position of inner region along X-axis
   YMAX	     [0.0]       : maximum position of inner region along Y-axis
   ZMAX	     [0.0]       : maximum position of inner region along Z-axis
   XMIN	     [0.0]       : minimum position of inner region along X-axis
   YMIN	     [0.0]       : minimum position of inner region along Y-axis
   ZMIN	     [0.0]       : minimum position of inner region along Z-axis
   SPHEre    [.FALSE.]   : spherical inner region
   SRDIst    [0.0]       : radius of spherical inner region
   RRXCen    [0.0]       : X position of spherical inner region 
   RRYCen    [0.0]       : Y position of spherical inner region 
   RRZCen    [0.0]       : Z position of spherical inner region 
 
   basis function-spec.:: [ [XNPOl integer] [YNPOl integer] [ZNPOl integer] ]
                          [NMPOl integer] 
                          [MAXNpol integer] [NLISt integer] [NOSOrt]
                          [CGSCal real]
   XNPOl     [0]         : number of Legendre polynomials in X direction
   YNPOl     [0]         : number of Legendre polynomials in Y direction
   ZNPOl     [0]         : number of Legendre polynomials in Z direction
   NMPOl     [0]         : number of multipoles with spherical harmonics
   MAXNpol   [NTPOL]     : maximum number of basis functions which are used in
                           the energy and forces calculations
   NLISt     [1]         : updating frequency for the ordered list of basis
                           functions during molecular dynamics
   NOSOrt    [.FALSE.]   : surpress the ordering of basis functions
   CGSCale   [1.0]       : charge scaling factor for the monopole basis
                           function
   
   large box-specifications:: [LBOX] [LDCEl real] [LNCEl integer] [FOCUS]
                                     [LXBCen real] [LYBCen real] [LZBCen real]
   LBOX      [.FALSE.]   : invoke large box calculation (see below)
   LDCEL     [4*DCEL]    : grid spacing of large box
   LNCEL     [33]        : number of grid point in 1D for a cubic large box
   LXBCEN    [0.0]       : the center of a large box in X
   LYBCEN    [0.0]       : the center of a large box in Y
   LZBCEN    [0.0]       : the center of a large box in Z
   FOCUS     [.FALSE.]   : use the potential from a large box calculation for
                           the boundary potential in finer calculation

2. Free energy decomposition
   The total electrostatic solvation energy is decomposed into G_oo, G_io, and
G_ii.  All decomposition calculations are performed using the PB solver.  
With G_io keyword we can calculate the static external field and save it using 
WRITE PHIX.  G_ii gives the exact reaction field energy with which we can 
compare the basis-set reaction field energy.


3. Inner region & Basis functions
   Currently, GSBP supports two shapes for the inner regions: an orthorhombic
rectangular box and a sphere.  For the rectangular box, Legendre polynomials
are used as a basis-set. The number of function along each cartesian axis can
be specified using XNPOL, YNPOL, and ZNPOL.  The resulting total number of
basis functions (NTPOL) is XNPOL*YNPOL*ZNPOL.  For the spherical inner region,
spherical harmonics are used.  The number of electric multipoles is specified
as NMPOL, and the resulting total number of basis functions (NTPOL) is
NMPOL*NMPOL (e.g., with NMPOL = 2 one is including the reaction field for the
monopole and dipole of the inner system).

   The calculation of the MIJ matrix can be done in a single job but can also
be restarted. This is convenient since one does not always know how many basis
functions would yield accurate results.  For example, one could calculate the
MIJ matrix with NMPOL=11 spherical harmonics.  After comparing the result with
exact PB reaction field, one may decide to increase the number of multipoles
in NMPOL.  This procedure is illustrated in the test case gsbptest1.inp.
The list of basis functions can be ordered and sorted such that the number of
multipole basis function used for the energy and force (MAXNpol) calculations
is reduced.  

The focussing method with a large initial box and interpolating boundary
condition (INTBP) is a necessary procedure for computing the MIJ matrix
because the charge distribution corresponding to a given basis function
involves a large number of lattice point charges. All grid points inside the
inner region contain a partial charge assigned by a basis function.
Therefore, it would take a long time to set the boundary potential directly.
In practice, the charges density from a basis function are interpolated onto
a large (coarse) grid to reduce the number of grid-point charges which 
increase the computational cost of setting up the boundary conditions.
In this case, the focussing method is much more useful because the boundary
potential can be obtained from the coarse grid calculation.



File: PBEQ ]-[ Node: Examples
Up: Top -=- Previous: GSBP -=- Next: Top\n


                                Examples

        This examples are meant to be a partial guide in setting up 
an input file for PBEQ. There are two test files, pbeqtest1.inp,
pbeqtest2.inp, pbeqtest3.inp, and pbeqtest7.inp.

Example (1) 
-----------
This example shows how to perform two PB calculations, one for a surrounding
dielectric of 80 (water) and one for a surrounding of 1.0 (vacuum).  The
difference between the two energies then corresponds to the electrostatic
contribution to the solvation free energy.  The salt concentration was zero
in this calculation.


PBEQ
 scalar wmain = radius

 SOLVE epsw 80.0 conc 0.0 ncel 30 dcel 0.4
 set ener80 = ?ENPB

 SOLVE epsw 1.0 
 set ener1 = ?ENPB

 CALC total = @ener80 - @ener1

 RESET
END


Example(2)
----------
This example shows how to use a set of atomic Born radii with a smoothing
window. 

set sw 0.4
set factor 0.939

PBEQ
 stream radius.str
 scalar wmain add @sw
 scalar wmain mult @factor
 scalar wmain set 0.0 sele type H* end
 scalar wmain show

 SOLVE epsw 80.0 ncel 100 dcel 0.3 -
       smooth swin @sw force sten 0.03 npbeq 1

 RESET          !! If you consider a minimization or dynamics with PB forces,
                !! don't use RESET here.
END


Example(3)
----------
This example shows how to set up a membrane potential and how to get 
the electrostatic contribution to the solvation free energy in the membrane 
environment.  Note that a non-zero concentration is required for a sensible
system with a membrane potential.

PBEQ
 scalar wmain = radius

 SOLVE epsw  80.0  ncel  150  dcel 0.5  conc  0.150  -
       Tmemb 25.0  Zmemb 0.0  epsm 2.0  vmemb 0.100
 set ener80 = ?ENPB
      
 SOLVE epsw 1.0    conc  0.000  -
       Tmemb 25.0  Zmemb 0.0  epsm 1.0  vmemb 0.000
 set ener1 = ?ENPB

 CALC total = @ener80 - @ener1

 RESET
END

Example(4)
----------
This example shows how to set up boundary potentials using FOCUS keyword,
how to read the saved potential, and how to calculate the electrostatic 
contribution to the solvation free energy using FOCUS.

PBEQ
 scalar wmain = radius
 
 SOLVE epsw 1.0 ncel 60 dcel 0.4
 open write file unit 40 name phi.dat
 write phi  unit 40

 SOLVE epsw 1.0 dcel 0.2 focus  ! boundary potentials from DCEL 0.4 potentials 

! NOTE: YOU CAN CHANGE NCEL IN THE FOCUSSED SYSTEM AS FOLLOWS;
!       SOLVE epsw 1.0 ncel 80 dcel 0.2 focus

 SOLVE epsw 1.0 dcel 0.1 focus  ! boundary potentials from DCEL 0.2 potentials

 open read  file unit 41 name phi.dat
 read  phi  unit 41

 SOLVE epsw 1.0 dcel 0.1 focus  ! boundary potentials from DCEL 0.4 potentials 

 RESET
END


PBEQ
 scalar wmain = radius

 SOLVE epsw 80.0 ncel 60 dcel 0.4
 set ener81 = ?ENPB

 SOLVE epsw 80.0 dcel 0.2 focus
 set ener82 = ?ENPB

 SOLVE epsw 80.0 dcel 0.1 focus
 set ener83 = ?ENPB

 SOLVE epsw 80.0 dcel 0.05 focus
 set ener84 = ?ENPB

 SOLVE epsw 1.0 dcel 0.4
 set ener11 = ?ENPB

 SOLVE epsw 1.0 dcel 0.2 focus
 set ener12 = ?ENPB

 SOLVE epsw 1.0 dcel 0.1 focus
 set ener13 = ?ENPB

 SOLVE epsw 1.0 dcel 0.05 focus
 set ener14 = ?ENPB

 calc total = @ener81 - @ener11
 calc total = @ener82 - @ener12
 calc total = @ener83 - @ener13
 calc total = @ener84 - @ener14

 SOLVE epsw 80.0 ncel 120 dcel 0.2
 set ener80 = ?ENPB

 SOLVE epsw 1.0
 set ener1 = ?ENPB
 calc total = @ener80 - @ener1      

 RESET
END


Example(5)
----------
This example shows pKa Poisson-Bolztmann calculations which
deals with explicit charge distribution on the ionizable site.
(see also ~chmtest/c28/pbeqtest7.inp)

! set residue for pKa calculation and the patch for the ionizable sidechain
set segid    = syst
set resid    = 2
set patch    = GLUP

!Miscelaneous variables 
set    Dcel   =  0.5 ! initial value for the mesh size in the finite-difference
set    Ncel   =   65 ! maximum number of grid points
set    EpsP   =  1.0 ! dielectric constant for the protein interior
set    EpsW   = 80.0 ! solvent dielectric constant  
set    Conc   =  0.0 ! salt concentration
set    Focus  = Yes

!Note that the resid must be set before streaming into this file

scalar wcomp = charge 

patch @patch @Segid @resid setup 

hbuild  !build any missing hydrogens

scalar wcomp  store 1
scalar charge store 2

define SITE select  .bygroup.  ( resid @resid ) show end
define REST select .not. site end

! Charges of the unprotonated state
scalar wmain recall 1 
scalar wmain show
scalar wmain stat select SITE end

! Charges of the protonated state
scalar wmain recall 2 
scalar wmain show
scalar wmain stat select SITE end

! Estimate the grid dimensions
format (f15.5)

coor orient norotate
coor stat select all end
calc DcelX = ( ?Xmax - ?Xmin ) / @Ncel
calc DcelY = ( ?Ymax - ?Ymin ) / @Ncel
calc DcelZ = ( ?Zmax - ?Zmin ) / @Ncel
if @DcelX gt @Dcel  set Dcel   = @DcelX
if @DcelY gt @Dcel  set Dcel   = @DcelY
if @DcelZ gt @Dcel  set Dcel   = @DcelZ

coor stat select SITE end
set Xcen = ?xave
set Ycen = ?yave
set Zcen = ?zave


PBEQ

stream @0radii.str

scalar charge recall 2    ! Protonated charge distribution

SOLVE ncel @Ncel Dcel @Dcel EpsP @epsP EpsW @EpsW  
if Focus eq yes -
SOLVE ncel @Ncel Dcel 0.25 EpsP @EpsP EpsW @EpsW  focus -
      XBcen @Xcen YBcen @Ycen ZBcen @Zcen

set EnerPs = ?enpb        ! Protonated side chain in structure

SOLVE ncel @Ncel Dcel @Dcel EpsP @epsP EpsW @EpsW  select SITE end 
if Focus eq yes -
SOLVE ncel @Ncel Dcel  0.25 EpsP @EpsP EpsW @EpsW  focus -
      XBcen @Xcen YBcen @Ycen ZBcen @Zcen select SITE end

set EnerPi = ?enpb        ! Protonated side chain isolated 

scalar charge recall 1    ! Unprotonated charge distribution

SOLVE ncel @Ncel Dcel @Dcel EpsP @epsP EpsW @EpsW  
if Focus eq yes -
SOLVE ncel @Ncel Dcel  0.25 EpsP @EpsP EpsW @EpsW  focus -
      XBcen @Xcen YBcen @Ycen ZBcen @Zcen

set EnerUs = ?enpb        ! Unprotonated side chain in structure

SOLVE ncel @Ncel Dcel @Dcel EpsP @epsP EpsW @EpsW  select SITE end 
if Focus eq yes 
SOLVE ncel @Ncel Dcel  0.25 EpsP @EpsP EpsW @EpsW  focus -
      XBcen @Xcen YBcen @Ycen ZBcen @Zcen select SITE end

set EnerUi = ?enpb        ! Unprotonated side chain isolated

calc Energy = ( @EnerPs - @EnerUs ) - ( @EnerPi - @EnerUi )

calc pKa = -@Energy/( ?KBLZ * 300.0 ) * log10(exp(1)) != log10(exp(-@Energy/(?KBLZ*300)))

END

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