___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, 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 | __________________ ____________________/ DelPhi II program started on Fri Aug 8 2008 at 11:19:16 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 17 atomic charges read from file fort.12 # of charge parameter records: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5725774 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -13.88300 48.29200 ymin,ymax (A): -27.17500 25.34100 zmin,zma (A): -29.86900 30.00800 x,y,z range (A): 62.17500 52.51600 59.87700 scale (grids/A): 0.5725774 object centre (A): 17.20450 -0.9169998 6.9499969E-02 number of atom coordinates read : 2766 total number of charged atoms : 2629 net assigned charge : 6.000009 assigned positive charge : 396.7086 centred at (gu) : 89.51380 89.75433 91.15289 assigned negative charge : -390.7095 centred at (gu) : 89.89642 90.07391 91.03336 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5929 nv = 96 ne = 84 npr = 59422 no. pairs analyzed = 59422 no. exposed pairs = 3932 no. arc points = 27421 no. surface atoms = 1330 nbur = 1436 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 284 mr = 2545 m= 0 mr = 13 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2799 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1724675E-08 8.4169933E-08 midg,1,midg; midg,igrid,midg 1.3908165E-07 -8.2595449E-08 1,midg,midg; igrid,midg,midg 1.6824285E-07 -9.9594764E-08 gauss-seidel spectral radius is 0.9890049 estimated iterations to convergence 78 setup time was (sec) 0.6200000 now iterating at: 11:19:16 rms-change max change #iterations 0.1277777 20.21854 at 10iterations 1.4930542E-02 2.299669 at 20iterations 2.2272104E-03 0.4081802 at 30iterations 5.4016610E-04 0.1066628 at 40iterations 1.7245140E-04 3.5205841E-02 at 50iterations finished qdiffx linear iterations at : 11:19:20 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 1.7245140E-04 3.5205841E-02 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 11:19:20 3.951u 0.337s 0:04.88 87.7% 0+0k 8+45936io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, 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 | __________________ ____________________/ DelPhi II program started on Fri Aug 8 2008 at 11:19:20 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 17 atomic charges read from file fort.12 # of charge parameter records: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.717732 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -13.88300 48.29200 ymin,ymax (A): -27.17500 25.34100 zmin,zma (A): -29.86900 30.00800 x,y,z range (A): 62.17500 52.51600 59.87700 scale (grids/A): 1.717732 object centre (A): 17.20450 -0.9169998 6.9499969E-02 number of atom coordinates read : 2766 total number of charged atoms : 2629 net assigned charge : 6.000009 assigned positive charge : 396.7086 centred at (gu) : 88.54070 89.26208 93.45819 assigned negative charge : -390.7095 centred at (gu) : 89.68882 90.22157 93.09969 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 63902 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27421 grid for indexing accessible points = 1.400000 m= 19566 mr = 39330 m= 2653 mr = 12165 m= 104 mr = 1195 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 33518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20388 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5725774 object centre at (A) : 17.20450 -0.9169998 6.9499969E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6747756E-03 2.6270727E-02 midg,1,midg; midg,igrid,midg 7.4894525E-02 -2.1657160E-02 1,midg,midg; igrid,midg,midg 8.2401313E-02 -6.9001168E-02 gauss-seidel spectral radius is 0.9987327 estimated iterations to convergence 222 setup time was (sec) 0.9200000 now iterating at: 11:19:22 rms-change max change #iterations 3.931202 188.5563 at 10iterations 1.889028 76.52679 at 20iterations 0.9052628 37.64279 at 30iterations 0.4352286 18.42781 at 40iterations 0.2095642 7.605982 at 50iterations 0.1008612 3.712523 at 60iterations 4.8665315E-02 1.793846 at 70iterations 2.3452632E-02 0.9018478 at 80iterations 1.1403481E-02 0.4518661 at 90iterations 5.6304638E-03 0.2058449 at 100iterations 2.8647413E-03 0.1180573 at 110iterations 1.5210158E-03 5.9707642E-02 at 120iterations finished qdiffx linear iterations at : 11:19:30 total time elapsed so far: 8.800000 # loops : 120 mean,max change (kT/e) : 1.5210158E-03 5.9707642E-02 energy calculations done at 8.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.970000 DelPhi exited at 11:19:31 8.972u 0.322s 0:10.09 92.0% 0+0k 672+45264io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, 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 | __________________ ____________________/ DelPhi II program started on Fri Aug 8 2008 at 11:19:31 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 17 atomic charges read from file fort.12 # of charge parameter records: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.576598 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -13.88300 48.29200 ymin,ymax (A): -27.17500 25.34100 zmin,zma (A): -29.86900 30.00800 x,y,z range (A): 62.17500 52.51600 59.87700 scale (grids/A): 2.576598 object centre (A): 17.20450 -0.9169998 6.9499969E-02 number of atom coordinates read : 2766 total number of charged atoms : 2629 net assigned charge : 6.000009 assigned positive charge : 396.7086 centred at (gu) : 87.81081 88.89297 95.18710 assigned negative charge : -390.7095 centred at (gu) : 89.53310 90.33223 94.64944 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 147953 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27421 grid for indexing accessible points = 1.400000 m= 64974 mr = 97637 m= 20876 mr = 47885 m= 4285 mr = 14636 m= 467 mr = 2689 m= 14 mr = 216 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.620000 number of dielectric boundary points 75506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 21019 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.717732 object centre at (A) : 17.20450 -0.9169998 6.9499969E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7789947E-02 0.2365654 midg,1,midg; midg,igrid,midg 0.5336188 -0.1817522 1,midg,midg; igrid,midg,midg 0.7388375 -0.9369462 gauss-seidel spectral radius is 0.9992790 estimated iterations to convergence 294 setup time was (sec) 1.930000 now iterating at: 11:19:33 rms-change max change #iterations 9.201164 322.9192 at 10iterations 5.432985 147.7842 at 20iterations 3.176341 69.23477 at 30iterations 1.853862 43.09796 at 40iterations 1.078182 24.27716 at 50iterations 0.6260119 15.14260 at 60iterations 0.3634354 7.951115 at 70iterations 0.2105220 4.756824 at 80iterations 0.1220897 2.487707 at 90iterations 7.0634864E-02 1.488245 at 100iterations 4.0833663E-02 0.8433571 at 110iterations 2.3679907E-02 0.4894905 at 120iterations 1.3732355E-02 0.2811050 at 130iterations 8.0111641E-03 0.1651592 at 140iterations 4.6842373E-03 9.7658157E-02 at 150iterations 2.7886298E-03 6.6774368E-02 at 160iterations 1.7001048E-03 4.0496826E-02 at 170iterations 1.0894382E-03 2.6836395E-02 at 180iterations finished qdiffx linear iterations at : 11:19:46 total time elapsed so far: 14.93000 # loops : 180 mean,max change (kT/e) : 1.0894382E-03 2.6836395E-02 energy calculations done at 14.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.10000 DelPhi exited at 11:19:47 15.103u 0.404s 0:15.98 96.9% 0+0k 44808+45272io 0pf+0w