    
  __________DelPhi V. 4 Release 1.0_______________  
 |                                                | 
 | A program to solve the PB equation             | 
 | in 3D, using non-linear form, incorporating    | 
 | many dielectric regions, multisalt ionic       | 
 | strength, different probe radii, periodic      | 
 | and focussing boundary conditions, utilizing   | 
 | stripped optimum successive over-relaxation    | 
 | and an improved algorithm for mapping the      | 
 | Mol. Surface to the finite-Difference grid     | 
 | Recompiled on Linux and PC                     | 
 |    January 2002 --------  Walter Rocchia       | 
 |__________________           ___________________| 
                    DelPhi V. 4                     
   
  program started on Wed Sep 29 2004
              at 17:50:59
 opening parameter file fort.10
 atom radii read from file
 Na.siz
  
 !this is amber 94 parameters defined by amber               
 !you can find charge in /usr/local/amber7/dat/leap/lib/ all_
 !you can find radii in /usr/local/amber7/dat/leap/parm parm9
 !THIS FILE ONLY INCLUDES THE AMINO ACID WHICH ARE INCLUDED I
 !NOT THE TOTAL 25 AMINO ACID                                
 # of radius parameter records:           1
  
 atomic charges read from file
 Na.crg
  
 !this is amber 94 parameters defined by amber               
 !you can find charge in /usr/local/amber7/dat/leap/lib/ all_
 !you can find radii in /usr/local/amber7/dat/leap/parm parm9
 !THIS FILE ONLY INCLUDES THE AMINO ACID WHICH ARE INCLUDED I
 !NOT THE TOTAL 25 AMINO ACID                                
 # of charge parameter records:           1
 assigning charges and radii...
  
 opening formatted file:Na.pdb
 You are not reading from an objectfile! assuming     having only molecules, and one dielectric medium
 number of atoms read in =            1
  
  
 Direct mapping of epsilon: (0/1)(n/y)           1
 time to read in and/or assign rad/chrg=  0.0000000E+00
 object number :              1,  is a molecule
 modifying midpoints using frc input file
   
 grid size                  :          81
 percent of box to be filled:   18.91646    
 scale,in grids/A :   4.000000    
 xmin,xmax     (A):   44.40000       48.13600    
 ymin,ymax     (A):   48.80100       52.53700    
 zmin,zmax     (A):   36.81400       40.55000    
 x,y,z range   (A):    3.736000       3.736000       3.736000    
 system geometric center in (A):   46.26800       50.66900       38.68200    
  grid  box is centered in (A) :   46.26800       50.66900       38.68200    
 object centred at (gu)     :   999.0000      0.0000000E+00  0.0000000E+00
 outer dielectric           :   80.00000    
 dielectric in medium number           1 :   1.000000    
 first kind salt concentration (M)   :  0.0000000E+00
 valences salt 1 are                   1 and           1
 second kind salt concentration (M)  :  0.0000000E+00
 valences salt 2 are                   0 and           0
 ionic strength (M)         :  0.0000000E+00
 debye length (A)           :   1000000.    
 ion exclusion radius (A)   :   1.824000    
 probe radius facing water(A:   1.400000    
 probe radius, internal (A) :   1.400000    
 boundary conditions        : dipolar  
 x,y,z periodic bc. flags   : F F F
 # of linear iterations     :        1200
 convergence by rms change :  1.0000000E-06 kt
 convergence by max change :  0.0000000E+00 kt
 # of non-linear iterations :           0
 non-linear energy calculat.: F
 manual relaxation parameter : F
 ionic direct energy contribution: F
 concentration map output   : F
 spherical charge distbn.   : F
 INSIGHT format output      : F
 site potential output      : F
 modified atom file output  : F
 map file label             :
qdiffxas: qdiffxs4 with an improved surfacing routine       
  convergence graph turned off
  potential listings turned off
  
 start vw surface at   0.0000000E+00
 Starting creating Vand der Waals  Epsilon Map 
 Ending creating Vand der Waals  Epsilon Map 
 fill in re-entrant regions at   0.0000000E+00
 boundary points facing continuum solvent=          582
 total number of boundary points before elab.=          582
 radpmax,radprb    1.400000       1.400000       1.400000    
 # of vertices =          384 # of edges =          372
 # of pairs =            0
 time to find all pairs =   0.0000000E+00
 # pairs analyzed (atom-atom and atom-object)=            0
 # exposed pairs (atom-atom and atom-object)=            0
 no. arc points  =            0
 no. surface atoms  =            1 nbur =            0
 mkacc time =   0.0000000E+00
 grid for indexing accessible points =    1.400000    
 bgp added m=           0 bgp removed  mr =           0
 time to grow re-entrant surface =   9.9999998E-03
 no. cavity mid-points inaccessible to solvent =            0
 after surface elaboration ibnum=          582
     and               ibnumsurf=          582
 scaling boundary grid points
 % of boundary points contacting solvent =    100.0000    
 time taken =   0.0000000E+00
            0 points had to be assigned by global comparison
 time to turn everything in is  9.9999998E-03
 number of charges coming from molecules            1
 number of charge distrib. present            0
   
 number of atom coordinates read  :            1
 total number of assigned charges    :            1
 net assigned charge              :    1.000000    
 assigned positive charge         :    1.000000    
 centred at (gu) :   41.00000       41.00000       41.00000    
 assigned negative charge         :   0.0000000E+00
 centred at (gu) :  0.0000000E+00  0.0000000E+00  0.0000000E+00
    
 number of dielectric boundary points         582
 no. dielectric boundary points in salt =            0
 no. grid points charged and not internal=           0
 iepsmp to db, and charging done at  9.9999998E-03
 number of grid points assigned charge           1
  
   setting boundary conditions
  
  some initial phi values: 
  midg,midg,1; midg,midg,igrid 
   0.7012430      0.7012430    
  midg,1,midg; midg,igrid,midg 
   0.7012430      0.7012430    
  1,midg,midg; igrid,midg,midg 
   0.7012430      0.7012430    
  
gauss-seidel spectral radius is        0.9983758926
  
 estimated iterations to convergence         197
   
 setup time was (sec)   3.9999999E-02
   
 now iterating at: 17:50:59
  
  
   rms-change     max change       #iterations
   1.3307604E+07   343.7390     at          10 iterations
    1778360.       171.1232     at          20 iterations
    305195.8       82.02722     at          30 iterations
    84657.93       33.35474     at          40 iterations
    14789.84       11.98901     at          50 iterations
    3049.537       4.881958     at          60 iterations
    526.3967       3.435547     at          70 iterations
    132.1794       2.186401     at          80 iterations
    20.46905      0.5616455     at          90 iterations
    3.334191      0.3208008     at         100 iterations
   0.6932200      8.6914063E-02 at         110 iterations
   0.1661398      7.9345703E-02 at         120 iterations
   2.0108592E-02  3.2958984E-02 at         130 iterations
   5.0005969E-03  1.8554688E-02 at         140 iterations
   1.2472497E-03  7.8125000E-03 at         150 iterations
   2.0329605E-04  1.4648438E-03 at         160 iterations
   4.5047542E-05  9.7656250E-04 at         170 iterations
   1.2335051E-05  3.6621094E-04 at         180 iterations
   2.6053226E-06  2.7465820E-04 at         190 iterations
   2.0604284E-06  2.4414063E-04 at         200 iterations
   1.4732341E-06  2.4414063E-04 at         210 iterations
   1.1844697E-06  1.8310547E-04 at         220 iterations
   7.1816083E-07  2.4414063E-04 at         230 iterations
 finished qdiffx linear iterations
 at                       : 17:51:01
 total time elapsed so far:    1.320000    
 # loops                  :          230
 mean,max change (kT/e)   :   7.1816083E-07  2.4414063E-04
  
 total grid energy          :        3413.200     kt
 self-reaction field energy :      3.6010849E-06 kt
 total s.charge,no epsin carrying :   -0.9875
 corrected reaction field energy:   -148.2792     kt
 total reaction field energy :     -148.2792     kt
  
 coulombic energy :                0.0000000E+00 kt
 All energy terms but grid and self_react.:  -148.2792    kt
 energy calculations done at   1.320000    
   
 writing potential map in DELPHI format
   
 potential map written to file
 fort.14                                                                         
   
   
 total cpu time was (sec)    1.320000    
   
 DelPhi exited at 17:51:01
