___________________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 Sep 18 2009 at 17:33:25 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: 18 atomic charges read from file fort.12 # of charge parameter records: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3538 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5932345 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 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): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 0.5932345 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3538 total number of charged atoms : 3390 net assigned charge : 2.000005 assigned positive charge : 540.2484 centred at (gu) : 88.74191 87.75149 89.96022 assigned negative charge : -538.2499 centred at (gu) : 88.74812 87.69319 89.92846 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7868 nv = 96 ne = 84 npr = 74698 no. pairs analyzed = 74698 no. exposed pairs = 4094 no. arc points = 28517 no. surface atoms = 1383 nbur = 2155 mkacc time = 0.2000000 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 = 1.456000 m= 354 mr = 4359 m= 0 mr = 26 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.4300000 number of dielectric boundary points 3837 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2969 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10279 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6223687E-10 2.0043176E-09 midg,1,midg; midg,igrid,midg -2.8354477E-09 1.8508324E-09 1,midg,midg; igrid,midg,midg 1.3176691E-09 3.6989789E-10 gauss-seidel spectral radius is 0.9853630 estimated iterations to convergence 68 setup time was (sec) 0.6900000 now iterating at: 17:33:26 rms-change max change #iterations 0.1195600 17.59710 at 10iterations 1.0002300E-02 1.446629 at 20iterations 8.3529024E-04 0.1188660 at 30iterations 7.1160714E-05 9.4127655E-03 at 40iterations 6.8823706E-06 9.0789795E-04 at 50iterations finished qdiffx linear iterations at : 17:33:30 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 6.8823706E-06 9.0789795E-04 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.940000 DelPhi exited at 17:33:31 3.949u 0.349s 0:05.15 83.1% 0+0k 0+46088io 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 Sep 18 2009 at 17:33:31 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: 18 atomic charges read from file fort.12 # of charge parameter records: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3538 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.779703 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 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): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 1.779703 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3538 total number of charged atoms : 3390 net assigned charge : 2.000005 assigned positive charge : 540.2484 centred at (gu) : 86.22511 83.25370 89.87994 assigned negative charge : -538.2499 centred at (gu) : 86.24400 83.07909 89.78513 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 87506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28517 grid for indexing accessible points = 1.400000 m= 29474 mr = 61862 m= 3712 mr = 21395 m= 141 mr = 2131 m= 0 mr = 29 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2330 time to turn everything in is 0.7300000 number of dielectric boundary points 35416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 258 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 26407 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) : 0.5932345 object centre at (A) : 74.44350 2.747000 27.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2576671E-02 -5.5062240E-03 midg,1,midg; midg,igrid,midg -5.5010156E-03 1.2184134E-02 1,midg,midg; igrid,midg,midg 2.9516403E-02 3.0278526E-02 gauss-seidel spectral radius is 0.9985187 estimated iterations to convergence 206 setup time was (sec) 1.010000 now iterating at: 17:33:32 rms-change max change #iterations 4.445867 152.0131 at 10iterations 2.018670 66.68480 at 20iterations 0.9132212 27.74471 at 30iterations 0.4159663 12.56503 at 40iterations 0.1885474 5.814651 at 50iterations 8.5721195E-02 2.705544 at 60iterations 3.8884372E-02 1.142344 at 70iterations 1.7695215E-02 0.6401997 at 80iterations 8.0451313E-03 0.2520866 at 90iterations 3.6550078E-03 0.1203880 at 100iterations 1.6608846E-03 5.0880432E-02 at 110iterations 7.5868942E-04 2.4553299E-02 at 120iterations finished qdiffx linear iterations at : 17:33:40 total time elapsed so far: 8.870000 # loops : 120 mean,max change (kT/e) : 7.5868942E-04 2.4553299E-02 energy calculations done at 8.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 17:33:41 9.046u 0.431s 0:10.53 89.9% 0+0k 0+45384io 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 Sep 18 2009 at 17:33:41 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: 18 atomic charges read from file fort.12 # of charge parameter records: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3538 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.669555 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 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): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 2.669555 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3538 total number of charged atoms : 3390 net assigned charge : 2.000005 assigned positive charge : 540.2484 centred at (gu) : 84.33740 79.88023 89.81976 assigned negative charge : -538.2499 centred at (gu) : 84.36596 79.61846 89.67746 start vw surface at 0.1800000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 202637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28517 grid for indexing accessible points = 1.400000 m= 99272 mr = 149837 m= 31729 mr = 81087 m= 6189 mr = 24914 m= 608 mr = 4506 m= 7 mr = 347 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 8260 time to turn everything in is 1.820000 number of dielectric boundary points 79751 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 27110 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) : 1.779703 object centre at (A) : 74.44350 2.747000 27.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2980301 -6.2346548E-02 midg,1,midg; midg,igrid,midg -0.2640228 5.8668438E-02 1,midg,midg; igrid,midg,midg 0.3677514 0.3946473 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 2.120000 now iterating at: 17:33:44 rms-change max change #iterations 10.75659 306.4907 at 10iterations 6.243857 133.1892 at 20iterations 3.603649 68.54929 at 30iterations 2.075938 44.15186 at 40iterations 1.191231 23.30783 at 50iterations 0.6835633 13.79577 at 60iterations 0.3919742 7.757410 at 70iterations 0.2245439 3.862049 at 80iterations 0.1284231 2.241292 at 90iterations 7.3425069E-02 1.367910 at 100iterations 4.1929875E-02 0.7306805 at 110iterations 2.3981566E-02 0.4089375 at 120iterations 1.3724070E-02 0.2552290 at 130iterations 7.8482861E-03 0.1396980 at 140iterations 4.4875997E-03 7.5353622E-02 at 150iterations 2.5601392E-03 4.5873642E-02 at 160iterations 1.4680130E-03 2.7347565E-02 at 170iterations 8.4517134E-04 1.6060591E-02 at 180iterations finished qdiffx linear iterations at : 17:33:57 total time elapsed so far: 15.14000 # loops : 180 mean,max change (kT/e) : 8.4517134E-04 1.6060591E-02 energy calculations done at 15.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.30000 DelPhi exited at 17:33:58 15.307u 0.468s 0:16.73 94.2% 0+0k 0+45392io 0pf+0w