___________________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 16:21:16 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 = 3535 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 : 3535 total number of charged atoms : 3387 net assigned charge : 2.000014 assigned positive charge : 541.3463 centred at (gu) : 88.75266 87.75268 89.96279 assigned negative charge : -539.3481 centred at (gu) : 88.75963 87.69534 89.93163 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 = 75449 no. pairs analyzed = 75449 no. exposed pairs = 4094 no. arc points = 28609 no. surface atoms = 1383 nbur = 2152 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 = 4362 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 0.4100000 number of dielectric boundary points 3845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2984 ## 358 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10278 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4115312E-10 1.9826363E-09 midg,1,midg; midg,igrid,midg -2.7780098E-09 1.8302556E-09 1,midg,midg; igrid,midg,midg 1.3541086E-09 3.4646380E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 16:21:17 rms-change max change #iterations 0.1192159 17.59689 at 10iterations 9.9840416E-03 1.444889 at 20iterations 8.3957444E-04 0.1141129 at 30iterations 7.5729607E-05 1.0303497E-02 at 40iterations 9.0220274E-06 1.1291504E-03 at 50iterations finished qdiffx linear iterations at : 16:21:20 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 9.0220274E-06 1.1291504E-03 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.880000 DelPhi exited at 16:21:21 3.888u 0.407s 0:05.13 83.4% 0+0k 832+46088io 2pf+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 16:21:21 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 = 3535 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 : 3535 total number of charged atoms : 3387 net assigned charge : 2.000014 assigned positive charge : 541.3463 centred at (gu) : 86.25737 83.25722 89.88765 assigned negative charge : -539.3481 centred at (gu) : 86.27854 83.08559 89.79474 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28609 grid for indexing accessible points = 1.400000 m= 29535 mr = 61815 m= 3733 mr = 21464 m= 140 mr = 2138 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 35524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 264 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 26383 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 -2.1612206E-02 -4.9551530E-03 midg,1,midg; midg,igrid,midg -5.4247035E-03 1.1807587E-02 1,midg,midg; igrid,midg,midg 2.9421842E-02 2.9011887E-02 gauss-seidel spectral radius is 0.9985191 estimated iterations to convergence 206 setup time was (sec) 0.9800000 now iterating at: 16:21:22 rms-change max change #iterations 4.462831 156.7497 at 10iterations 2.028222 65.03734 at 20iterations 0.9169719 28.05565 at 30iterations 0.4185388 12.69709 at 40iterations 0.1894384 5.822284 at 50iterations 8.6123750E-02 2.517372 at 60iterations 3.9087102E-02 1.125345 at 70iterations 1.7766515E-02 0.6715508 at 80iterations 8.0718976E-03 0.2591820 at 90iterations 3.6714976E-03 0.1361275 at 100iterations 1.6712990E-03 5.1334381E-02 at 110iterations 7.6234085E-04 2.6989937E-02 at 120iterations finished qdiffx linear iterations at : 16:21:30 total time elapsed so far: 8.990000 # loops : 120 mean,max change (kT/e) : 7.6234085E-04 2.6989937E-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) 9.100000 DelPhi exited at 16:21:31 9.107u 0.476s 0:10.05 95.2% 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 16:21:31 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 = 3535 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 : 3535 total number of charged atoms : 3387 net assigned charge : 2.000014 assigned positive charge : 541.3463 centred at (gu) : 84.38578 79.88550 89.83130 assigned negative charge : -539.3481 centred at (gu) : 84.41782 79.62822 89.69186 start vw surface at 0.1800000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 202700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28609 grid for indexing accessible points = 1.400000 m= 99404 mr = 149709 m= 31852 mr = 81183 m= 6195 mr = 25021 m= 606 mr = 4520 m= 8 mr = 348 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 79984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 27086 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 -0.2841831 -5.7269543E-02 midg,1,midg; midg,igrid,midg -0.2635426 5.4030076E-02 1,midg,midg; igrid,midg,midg 0.3657379 0.3729864 gauss-seidel spectral radius is 0.9992434 estimated iterations to convergence 287 setup time was (sec) 2.120000 now iterating at: 16:21:33 rms-change max change #iterations 10.80768 306.6386 at 10iterations 6.279382 161.1649 at 20iterations 3.622461 70.09569 at 30iterations 2.088206 40.80960 at 40iterations 1.199383 22.35277 at 50iterations 0.6880414 14.06411 at 60iterations 0.3946798 7.586843 at 70iterations 0.2261270 3.868988 at 80iterations 0.1293460 2.167021 at 90iterations 7.3974170E-02 1.302597 at 100iterations 4.2224649E-02 0.7248745 at 110iterations 2.4185091E-02 0.4074790 at 120iterations 1.3833676E-02 0.2327976 at 130iterations 7.9205856E-03 0.1505165 at 140iterations 4.5309300E-03 7.5012207E-02 at 150iterations 2.5878535E-03 4.2966366E-02 at 160iterations 1.4843782E-03 2.5506020E-02 at 170iterations 8.5549755E-04 1.6023636E-02 at 180iterations finished qdiffx linear iterations at : 16:21:47 total time elapsed so far: 15.34000 # loops : 180 mean,max change (kT/e) : 8.5549755E-04 1.6023636E-02 energy calculations done at 15.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.48000 DelPhi exited at 16:21:47 15.484u 0.465s 0:16.47 96.7% 0+0k 0+45392io 0pf+0w