 |
|
|
$PCMCAV group (optional)
This group controls generation of the cavity holding the
solute during Polarizable Continuum Model runs. The cavity
is a union of spheres, according to NESFP given in $PCM.
The data in this group supplements cavity data given in
$PCM. It is unlikely that users will input anything here,
except perhaps a few RIN values. The data given here must
be in Angstrom units.
XE,YE,ZE = arrays giving the coordinates of the spheres.
if NESFP=0, the atomic positions will be used.
if NESFP>0, you must supply NESFP values here.
RADII = three tables of values (Angstroms!) are available:
VANDW selects van der Waals radii (default)
This table has radii for atoms
H,He, B,C,N,O,F,Ne, Na,Al,Si,P,S,Cl,Ar,
K,As,Se,Br,Kr, Rb,Sb,Te,I, Cs,Bi
internally tabulated, otherwise give RIN.
= VDWEFP, similar to VANDW, except that radii not
tabulated by VANDW are assigned as 1.60A.
This option is most useful for protein-EFP
calculations.
= SUAHF, the simplified united atomic radii will be
be used for the array RIN, namely
H:0.01 C:1.77 N:1.68 O:1.59 P:2.10 S:2.10
For the other elements with Z<16, 1.50 is used.
For the elements with Z>16, 2.30 will be applied.
RIN = an array giving the sphere radii. Radii given here
will overwrite the values selected by RADII's tables.
RIN values are multiplied by ALPHA, see just below.
if NESFP=0, the program will look up the internally
data according to the RADII keyword.
if NESFP>0, give NESFP values.
Example: Suppose the 4th atom in your molecule is Fe, but
all other atoms have van der Waals radii. You
decide a good guess for Fe is twice the covalent
radius: $PCMCAV RIN(4)=2.33 $END. Due to ALPHA,
traditionally 1.2, the Fe radius will be 2.796.
The source for the van der Waals radii is "The Elements",
2nd Ed., John Emsley, Clarendon Press, Oxford, 1991, except
for C,N,O where the Pisa group's experience with the best
radii for PCM treatment of singly bonded C,N,O atoms is
taken. The radii for a few transition metals are given by
A.Bondi, J.Phys.Chem. 68, 441-451(1964).
ALPHA = an array of scaling factors, for the definition of
the solvent accessible surface. If only the first
value is given, all radii are scaled by the same
factor. (default is ALPHA(1)=1.2)
EPSHET = an array of dielectric constants, for each atom
in the heterogeneous CPCM. The default is to use
the same dielectric for every atom, namely the
value of EPS in $PCM. (only if IEF=10 or -10).
The default EPSHET(1)=X,X,X,X where EPS=X means
homogeneous CPCM.
==========================================================
==========================================================
generated on 7/7/2017