!==================================
! Example delphi default parameter file
!==================================
! SYNTAX: 
! Keywords are case insensitive. ascii strings used for file names are
! case sensitive
! Everything after # or ! on a line is ignored as a comment.
! Other lines contain 'phrases' of the form: keyword=value
! with no spaces between  keyword, equal sign and value.
! Phrases are delimited by one or more spaces or commas, or by the end of
! a line- a phrase must therefore fit on one line. More than one phrase
! may be placed on a line.  Each phrase contains a keyword, and a value.
! The value is either a real number, integer, a logical (t or f) or
! an ascii string containing no blanks or commas, depending on what type
! of variable the keyword is.  Unparseable phrases, 
! unrecognized keywords or invalid values types are ignored.
! Repeated assignments of a value to the same keyword will overwrite
! its value.  Delphi will first read this file, then try to read
! a specific parameter file of indentical format which is 
! named on the command line invoking the program. In this way
! defaults may be overridden.  All parameters must be assigned, except
! when they are made redundant by various options. Some of these
! are indicated in the comments below by option A, option B etc.
! Others should be obvious, i.e if no focussing is used, then an
! input phimap filename is not needed.
! Keywords may be abbreviated: the redundant letters are indicated
! in the file delphi_parm.lis, which has an alphabetical listing of
! parameters, and also output file by the letters after the 
! asterisk in the keyword name.  For purposes of illustration this
! file contains a default for every parameter. In actual usage you would
! probably not have defaults for everything, especially file names, and
! so would deleted the appropriate entries from this file
!
! grid and scaling parameters
!
gridsize=65          
!
!==================================
! scaling options
!==================================
!
!sizing=scale scale=1.0  xcen=0.0000  ycen=0.0000  zcen=0.0000    !option A
!sizing=fill  fill=96                                             !option B
sizing=border border_solvent=10.                                  !option C
!
!==================================
! boundary condition options
!==================================
!
boundary_condition=coulombic            !option A
!boundary_condition=focussing            !option B
!boundary_condition=zero                 !option C
!boundary_condition=field                !option D
!boundary_condition=dipolar              !option E
xperiodic=f               yperiodic=f            zperiodic=f
!
!==================================
! solute parameters
!==================================
!
solute_dielectric=2.     spherical_charge_dist=f        
!
!==================================
! solvent parameters
!==================================
!
solvent_dielectric=80.    salt_concentration=0.145
probe_radius=1.4          ionic_radius=2.0

!
!==================================
! algorithm parameters
!==================================
!
temperature=298.
nonlinear_equation=t        
convergence=0.001 relaxation_parameter=1.0
check_frequency=2        
newton_iterations=20
level0_multi_grid_it=2    level1_multi_grid_it=4
level2_multi_grid_it=8    level3_multi_grid_it=16
smooth_dielectric=0 
!
!==================================
! output parameters
!==================================
!
concentration_output=f         
insight_format=f         
site_potentials=f        
atom_file_output=f       
analyse_map=f
title=untitled
!
!=============================
! input files. Note input, output defaults are set up so that they would
! read from the appropriate linked files in oldstyle delphi input method
!=============================
!
radius_file=rna2.siz
charge_file=amber.crg
!site_charge_file=fort.12
pdb_input_file=xxx.pdb
!phi_input_file=xxx.phi
!site_input_file=xxx.pdb
!
!=============================
! output files
!=============================
!
!pdb_output_file=xxx.mod
phi_output_file=xxx.phi
dielectric_map_file=fort.17
!site_output_file=xxx.pdb