my_Ndiel_solver is similar to the other electrostatic
potential solver programs, with the exception that the
number of dielectric and electrolyte regions is not
limited. Solvent accessible volumes and ion inaccessible
volumes can be defined with pqr files that contain either
true molecular coordinates or artificial volumes defined
by dummy atoms. Usage of the other solver programs is similar --
usage examples are included in the examples for gcem
see gcem_input/gcem/job.sh created by GCEM.

The program is called with

/mead_path/apps/my_Ndiel_solver/my_Ndiel_solver {additional options} -fpt site sitename molname

where sitename and molname are prefixes of pqr files that
correspond to site / group and molname, respectively.
sitename denotes the site or group for which the electrostatic
energy within the molecule molname shall be calculated.
The computed electrostatic potential originates solely from
the atomic partial charges in sitename.pqr. If you want to
compute the electrostatic potential of the whole molecule, you
can include it completely in sitename.pqr.
Site is the prefix of the file site.fpt. This file contains the atomic
coordinates and atomic partial charges of the forms / instances
of other sites within molname, that are used to calculate the
interaction energies of the other sites in their respective instances
with sitename.

Note that the solvation / Born energy of sitename in molname
is not free of grid artifacts. That is, only differences of
solvation energies relative to some reference state are meaningful.
Often, the reference state will be sitename in vacuum or bulk solvent.
You can compute the solvation energy of the reference state with
one of the solver programs my_Xdiel_solver or my_memb_solver.
It is necessary to use identical settings for the innermost grid
(at least grid spacing and grid center) to obtain cancellation of
grid artifacts.


The dielectric regions are defined in molname.diel,
where pqr_name_X is the prefix of a .pqr file defining
region X eps_X is the dielectric constant (relative
dielectric permittivity) of the region and solvent_radius_X
is the radius of the solvent surrounding region X.

format:

pqr_name_1   eps_1   solvent_radius_1
pqr_name_2   eps_2   solvent_radius_2
...
pqr_name_N   eps_N   solvent_radius_N

The importance increases from 1 to N, that is preceding
dielectric regions are overridden.

For the treatment of nested regions, it is advisable to
include the atoms defining the embedded regions in the
pqr files of the surrounding regions and to place embedded
regions after the corresponding surrounding regions on
the list. In this way, one can avoid spurious occurrences
of solvent dielectric at the interface of dielectric regions.

Similarly, the electrolyte regions are defined in molname.ely,
where pqr_name_X is the prefix of a .pqr file defining
region X ionic_strength_X is the ionic streng in mol/l outside
the region and stern_layer_radius_X is the is the typical radius
of the mobile ions in the solvent surrounding region X.

format:

pqr_name_1   ionic_strenght_1   stern_layer_radius_1
pqr_name_2   ionic_strenght_2   stern_layer_radius_2
...
pqr_name_N   ionic_strenght_N   stern_layer_radius_N

Importance increases from 1 to N, that is preceding
electrolyte regions are overridden. 

It is necessary to include the atoms defining the
embedded regions in the pqr files of the surrounding regions
and to place embedded regions after the corresponding surrounding
regions on the list. This is, because the ionic strength outside
region X overrides the ionic strength outside all preceding regions
1, .., X-1.

The example electrolyte regions are chosen for the sake of simplicity,
but not for realism. A region around mm_region of thicknesss 5 A
is filled with a different electrolyte than the solvent outside
this region.
