___________________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 Mon May 16 2011 at 10:21:33 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: 285 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= 7.9999998E-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 : 2.000014 assigned positive charge : 541.3802 centred at (gu) : 88.74930 87.75592 89.95528 assigned negative charge : -539.3821 centred at (gu) : 88.75515 87.69872 89.92462 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7880 nv = 96 ne = 84 npr = 75514 no. pairs analyzed = 75514 no. exposed pairs = 4085 no. arc points = 28552 no. surface atoms = 1382 nbur = 2156 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= 353 mr = 4367 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 0.4000000 number of dielectric boundary points 3840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2978 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10278 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2084786E-10 1.9596116E-09 midg,1,midg; midg,igrid,midg -2.7656264E-09 1.8286825E-09 1,midg,midg; igrid,midg,midg 1.2949766E-09 3.8052470E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6400000 now iterating at: 10:21:34 rms-change max change #iterations 0.1193452 17.59689 at 10iterations 9.9792210E-03 1.448978 at 20iterations 8.3685340E-04 0.1191301 at 30iterations 7.2576739E-05 9.8724365E-03 at 40iterations 7.4954696E-06 1.0604858E-03 at 50iterations finished qdiffx linear iterations at : 10:21:37 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 7.4954696E-06 1.0604858E-03 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 10:21:38 3.902u 0.388s 0:05.19 82.4% 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 Mon May 16 2011 at 10:21:38 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: 285 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 : 2.000014 assigned positive charge : 541.3802 centred at (gu) : 86.24726 83.26692 89.86510 assigned negative charge : -539.3821 centred at (gu) : 86.26513 83.09575 89.77370 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87602 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28552 grid for indexing accessible points = 1.400000 m= 29515 mr = 61879 m= 3712 mr = 21454 m= 139 mr = 2125 m= 0 mr = 29 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 2330 time to turn everything in is 0.7000000 number of dielectric boundary points 35481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 iepsmp to db, and charging done at 0.8300000 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 -2.1920430E-02 -5.2242819E-03 midg,1,midg; midg,igrid,midg -5.4453197E-03 1.1848497E-02 1,midg,midg; igrid,midg,midg 2.9411217E-02 2.9812394E-02 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 0.9800000 now iterating at: 10:21:40 rms-change max change #iterations 4.455968 159.4855 at 10iterations 2.024980 65.03343 at 20iterations 0.9155852 27.83265 at 30iterations 0.4178463 12.63464 at 40iterations 0.1891615 5.835784 at 50iterations 8.6008050E-02 2.533456 at 60iterations 3.9024893E-02 1.170498 at 70iterations 1.7737487E-02 0.6628971 at 80iterations 8.0614723E-03 0.2571945 at 90iterations 3.6658123E-03 0.1311359 at 100iterations 1.6673708E-03 5.1826477E-02 at 110iterations 7.6060992E-04 2.5347710E-02 at 120iterations finished qdiffx linear iterations at : 10:21:48 total time elapsed so far: 8.990000 # loops : 120 mean,max change (kT/e) : 7.6060992E-04 2.5347710E-02 energy calculations done at 8.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.160000 DelPhi exited at 10:21:49 9.169u 0.413s 0:10.49 91.2% 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 Mon May 16 2011 at 10:21:49 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: 285 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= 7.9999998E-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 : 2.000014 assigned positive charge : 541.3802 centred at (gu) : 84.37061 79.90004 89.79749 assigned negative charge : -539.3821 centred at (gu) : 84.39769 79.64346 89.66029 start vw surface at 0.1800000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 202796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28552 grid for indexing accessible points = 1.400000 m= 99417 mr = 149838 m= 31759 mr = 81234 m= 6154 mr = 24945 m= 604 mr = 4496 m= 7 mr = 347 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 8260 time to turn everything in is 1.840000 number of dielectric boundary points 79877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 2.000000 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 -0.2895196 -6.0245987E-02 midg,1,midg; midg,igrid,midg -0.2634574 5.4471813E-02 1,midg,midg; igrid,midg,midg 0.3657672 0.3875865 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 2.170000 now iterating at: 10:21:51 rms-change max change #iterations 10.79290 306.6191 at 10iterations 6.267757 160.4543 at 20iterations 3.613564 71.30498 at 30iterations 2.082105 40.42921 at 40iterations 1.195107 22.88764 at 50iterations 0.6851991 14.15568 at 60iterations 0.3929862 7.626995 at 70iterations 0.2251778 3.865294 at 80iterations 0.1287430 2.141177 at 90iterations 7.3613234E-02 1.277847 at 100iterations 4.2023610E-02 0.7739372 at 110iterations 2.4053436E-02 0.4312923 at 120iterations 1.3754054E-02 0.2447963 at 130iterations 7.8716455E-03 0.1571960 at 140iterations 4.5003882E-03 8.1502914E-02 at 150iterations 2.5701828E-03 4.5348167E-02 at 160iterations 1.4735310E-03 2.4011612E-02 at 170iterations 8.4855739E-04 1.6468048E-02 at 180iterations finished qdiffx linear iterations at : 10:22:06 total time elapsed so far: 15.51000 # loops : 180 mean,max change (kT/e) : 8.4855739E-04 1.6468048E-02 energy calculations done at 15.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.68000 DelPhi exited at 10:22:06 15.690u 0.407s 0:17.50 91.9% 0+0k 0+45392io 0pf+0w