modified on 11 October 2016 at 16:56 ••• 3,859 views

Release66:ESP

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Electrostatic potentials

The NWChem Electrostatic Potential (ESP) module derives partial atomic charges that fit the quantum mechanical electrostatic potential on selected grid points.

The ESP module is specified by the NWChem task directive

task esp

The input for the module is taken from the ESP input block

ESP
  ...
END

Grid specification

The grid points for which the quantum mechanical electrostatic potential is evaluated and used in the fitting procedure of the partial atomic charges all lie outside the van der Waals radius of the atoms and within a cutoff distance from the atomic centers. The following input parameters determine the selection of grid points.

  • If a grid file is found, the grid will be read from that file. If no grid file is found, or the keyword
       recalculate

     is given, the grid and the electrostatic potential is recalculated.
  • The extent of the grid is determined by
       range <real rcut>

     where rcut is the maximum distance in nm between a grid point and any of the atomic centers. 
     When omitted, a default value for rcut of 0.3 nm is used.
  • The grid spacing is specified by
       spacing <real spac>

     where spac is the grid spacing in $nm$ for the regularly spaced grid points. 
     If not specified, a default spacing of 0.05 nm is used.
  • The van der Waals radius of an element can be specified by
       radius <integer iatnum> <real atrad>

     where iatnum is the atomic number for which a van der Waals radius of atrad in nm will be used in 
     the grid point determination. Default values will be used for atoms not specified.
  • The probe radius in nm determining the envelope around the molecule is specified by
       probe <real probe default 0.07>
  • The distance between atomic center and probe center can be multiplied by a constant factor specified by
       factor <real factor default 1.0>

     All grid points are discarded that lie within a distance factor*(radius(i)+probe) from any atom i.
  • Schwarz screening is applied using
       screen [<real scrtol default 1.0D-5>]

Constraints

Additional constraints to the partial atomic charges can be imposed during the fitting procedure.

  • The net charge of a subset of atoms can be constrained using
       constrain <real charge> {<integer iatom>}

     where charge is the net charge of the set of atoms {iatom}. A negative atom number iatom can be 
     used to specify that the partial charge of that atom is substracted in the sum for the set.
  • The net charge of a sequence of atoms can be constrained using
       constrain <real charge> <integer iatom> through <integer jatom>

     where charge is the net charge of the set of atoms {[iatom:jatom]}.
  • A group of atoms can be constrained to have the same charge with
       constrain equal {<integer iatom>}
  • The individual charge of a group of atoms can be constrained to be equal to those of a second group of atoms with
       constrain group <integer iatom> <integer jatom> to <integer katom> <integer latom>

     resulting in the same charge for atoms iatom and katom, for atoms iatom+1 and k
     atom+1, ... for atoms jatom and latom.
  • A special constraint
       constrain xhn <integer iatom> {<integer jatom>}

     can be used to constrain the set {iatom,{jatom}} to zero charge, and constrain all atoms 
     in {jatom} to have the same charge. This can be used, for example, to restrain a methyl 
     group to zero charge, and have all hydrogen carrying identical charges.

Restraints

Restraints can be applied to each partial charge using the RESP charge fitting procedure.

  • The directive for charge restraining is
       restrain [hfree] (harmonic [<real scale>] | \
        hyperbolic [<real scale> [<real tight>]]  \
         [maxiter <integer maxit>]  [tolerance <real toler>])

Here hfree can be specified to exclude hydrogen atoms from the restaining procedure. Variable scale is the strength of the restraint potential, with a default of 0.005 au for the harmonic restraint and a default value of 0.001 au for the hyperbolic restraint. For the hyperbolic restraints the tightness tight can be specified to change the default value of 0.1 e. The iteration count that needs to be carried out for the hyperbolic restraint is determined by the maximum number of allowed iterations maxiter, with a default value of 25, and the tolerance in the convergence of the partial charges toler, with a default of 0.001 e.

Plotting

The electrostatic potential computed on a grid can be displayed using the gOpenMol [1] code.

A necessary step requires to convert the .plt file computed by the ESP module from human readable to machine readable format; this can be achieved by using the gOpenMol Pltfile converter.

In practice, you would need to follow the following steps

  1. rename filename.plt to filename.plt.txt
  2. start gOpenMol
  3. open the Run menu
  4. select the Pltfile (conversion) utility
  5. choose filename.plt.txt as input file name and filename.plt as the output file name
  6. select Formatted ==> Unformatted
  7. read the filename.xyz file by going to: File -> Import -> Coord -> Browse -> Apply; you should see your system in the main graphical window as connections between atoms
  8. plot the density by going to Plot -> Contour
  9. first click Browse and read the gOpenMol filename.plt file:
  10. then click Import
  11. define desired Contour level
  12. click Apply

More details at: http://nms.kcl.ac.uk/lev.kantorovitch/codes/lev00/node71.html