___________________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 Tue May 17 2011 at 11:10:16 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: 18 atomic charges read from file fort.12 # of charge parameter records: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3529 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 : 3529 total number of charged atoms : 3381 net assigned charge : 2.000014 assigned positive charge : 539.1123 centred at (gu) : 88.73666 87.73935 89.97157 assigned negative charge : -537.1141 centred at (gu) : 88.74350 87.68259 89.93954 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7879 nv = 96 ne = 84 npr = 75332 no. pairs analyzed = 75332 no. exposed pairs = 4108 no. arc points = 28734 no. surface atoms = 1388 nbur = 2141 mkacc time = 0.1900000 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= 355 mr = 4357 m= 0 mr = 26 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.4200000 number of dielectric boundary points 3851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2983 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10262 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7090732E-10 2.0153550E-09 midg,1,midg; midg,igrid,midg -2.7309839E-09 1.8049799E-09 1,midg,midg; igrid,midg,midg 1.3495138E-09 3.4962472E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 11:10:17 rms-change max change #iterations 0.1189563 17.59689 at 10iterations 9.9550514E-03 1.423565 at 20iterations 8.4234722E-04 0.1141243 at 30iterations 8.1379658E-05 1.1045456E-02 at 40iterations 1.2232980E-05 1.4610291E-03 at 50iterations finished qdiffx linear iterations at : 11:10:20 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 1.2232980E-05 1.4610291E-03 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 11:10:21 3.891u 0.388s 0:04.90 87.1% 0+0k 608+46088io 1pf+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 Tue May 17 2011 at 11:10:21 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3529 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: 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 : 3529 total number of charged atoms : 3381 net assigned charge : 2.000014 assigned positive charge : 539.1123 centred at (gu) : 86.20938 83.21725 89.91400 assigned negative charge : -537.1141 centred at (gu) : 86.23016 83.04733 89.81847 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87511 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28734 grid for indexing accessible points = 1.400000 m= 29525 mr = 61715 m= 3742 mr = 21441 m= 139 mr = 2144 m= 0 mr = 29 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2330 time to turn everything in is 0.7000000 number of dielectric boundary points 35588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 264 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 26342 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 -2.1807531E-02 -4.8664524E-03 midg,1,midg; midg,igrid,midg -5.2571767E-03 1.1740566E-02 1,midg,midg; igrid,midg,midg 2.9434092E-02 2.9153408E-02 gauss-seidel spectral radius is 0.9985192 estimated iterations to convergence 206 setup time was (sec) 0.9800000 now iterating at: 11:10:22 rms-change max change #iterations 4.451916 152.0337 at 10iterations 2.022521 65.04325 at 20iterations 0.9146415 28.24304 at 30iterations 0.4173610 12.67468 at 40iterations 0.1890488 5.908499 at 50iterations 8.6010687E-02 2.528631 at 60iterations 3.9053231E-02 1.093435 at 70iterations 1.7740356E-02 0.6411972 at 80iterations 8.0644507E-03 0.2647820 at 90iterations 3.6696999E-03 0.1295795 at 100iterations 1.6696607E-03 5.2215576E-02 at 110iterations 7.6276180E-04 2.6457787E-02 at 120iterations finished qdiffx linear iterations at : 11:10:30 total time elapsed so far: 8.860000 # loops : 120 mean,max change (kT/e) : 7.6276180E-04 2.6457787E-02 energy calculations done at 8.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.970000 DelPhi exited at 11:10:31 8.977u 0.474s 0:09.90 95.3% 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 Tue May 17 2011 at 11:10:31 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3529 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 : 3529 total number of charged atoms : 3381 net assigned charge : 2.000014 assigned positive charge : 539.1123 centred at (gu) : 84.31381 79.82551 89.87084 assigned negative charge : -537.1141 centred at (gu) : 84.34526 79.57085 89.72746 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 202553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28734 grid for indexing accessible points = 1.400000 m= 99318 mr = 149456 m= 31867 mr = 81070 m= 6224 mr = 25038 m= 608 mr = 4539 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 1.800000 number of dielectric boundary points 80127 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 27038 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 -0.2873535 -5.6193732E-02 midg,1,midg; midg,igrid,midg -0.2617216 5.3685311E-02 1,midg,midg; igrid,midg,midg 0.3659199 0.3747357 gauss-seidel spectral radius is 0.9992442 estimated iterations to convergence 287 setup time was (sec) 2.100000 now iterating at: 11:10:33 rms-change max change #iterations 10.77333 306.7222 at 10iterations 6.262408 161.2582 at 20iterations 3.615466 78.94487 at 30iterations 2.086385 42.09302 at 40iterations 1.199868 22.48075 at 50iterations 0.6883933 14.06620 at 60iterations 0.3950218 7.130557 at 70iterations 0.2265413 3.844698 at 80iterations 0.1296540 2.330507 at 90iterations 7.4193612E-02 1.339222 at 100iterations 4.2396199E-02 0.7740283 at 110iterations 2.4292639E-02 0.4548788 at 120iterations 1.3892532E-02 0.2569919 at 130iterations 7.9641845E-03 0.1565142 at 140iterations 4.5601381E-03 7.8810215E-02 at 150iterations 2.6064736E-03 4.5516968E-02 at 160iterations 1.4976484E-03 2.6612282E-02 at 170iterations 8.6402701E-04 1.5493393E-02 at 180iterations finished qdiffx linear iterations at : 11:10:46 total time elapsed so far: 15.21000 # loops : 180 mean,max change (kT/e) : 8.6402701E-04 1.5493393E-02 energy calculations done at 15.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.35000 DelPhi exited at 11:10:47 15.356u 0.473s 0:16.34 96.8% 0+0k 0+45392io 0pf+0w