___________________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 Wed Sep 30 2009 at 15:35:24 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3541 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 : 3541 total number of charged atoms : 3393 net assigned charge : 2.000013 assigned positive charge : 541.4822 centred at (gu) : 88.75510 87.76089 89.96188 assigned negative charge : -539.4841 centred at (gu) : 88.76051 87.70292 89.92920 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7879 nv = 96 ne = 84 npr = 75548 no. pairs analyzed = 75548 no. exposed pairs = 4080 no. arc points = 28533 no. surface atoms = 1377 nbur = 2164 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 = 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 0.4100000 number of dielectric boundary points 3840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2981 ## 359 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10290 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0335453E-10 2.0451734E-09 midg,1,midg; midg,igrid,midg -2.8159888E-09 1.8504451E-09 1,midg,midg; igrid,midg,midg 1.2705363E-09 3.9521492E-10 gauss-seidel spectral radius is 0.9853627 estimated iterations to convergence 68 setup time was (sec) 0.6700000 now iterating at: 15:35:25 rms-change max change #iterations 0.1197584 17.59671 at 10iterations 9.9836681E-03 1.454571 at 20iterations 8.3420204E-04 0.1181965 at 30iterations 7.0533351E-05 9.7332001E-03 at 40iterations 6.6143289E-06 9.8800659E-04 at 50iterations finished qdiffx linear iterations at : 15:35:29 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 6.6143289E-06 9.8800659E-04 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.960000 DelPhi exited at 15:35:30 3.966u 0.411s 0:05.19 84.2% 0+0k 904+46096io 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 Wed Sep 30 2009 at 15:35:30 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3541 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 : 3541 total number of charged atoms : 3393 net assigned charge : 2.000013 assigned positive charge : 541.4822 centred at (gu) : 86.26470 83.28185 89.88496 assigned negative charge : -539.4841 centred at (gu) : 86.28119 83.10833 89.78744 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28533 grid for indexing accessible points = 1.400000 m= 29510 mr = 61921 m= 3709 mr = 21442 m= 139 mr = 2126 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 0.7100000 number of dielectric boundary points 35456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 26433 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 -2.2833675E-02 -5.0350009E-03 midg,1,midg; midg,igrid,midg -5.3978506E-03 1.2184949E-02 1,midg,midg; igrid,midg,midg 2.9479044E-02 3.0147415E-02 gauss-seidel spectral radius is 0.9985188 estimated iterations to convergence 206 setup time was (sec) 1.000000 now iterating at: 15:35:31 rms-change max change #iterations 4.452558 152.0177 at 10iterations 2.022907 64.98667 at 20iterations 0.9145697 27.64819 at 30iterations 0.4169953 12.62885 at 40iterations 0.1889697 5.837041 at 50iterations 8.5918069E-02 2.636665 at 60iterations 3.9011080E-02 1.153748 at 70iterations 1.7699156E-02 0.6114807 at 80iterations 8.0551421E-03 0.2513018 at 90iterations 3.6600945E-03 0.1284008 at 100iterations 1.6653605E-03 5.1898956E-02 at 110iterations 7.5968076E-04 2.4785995E-02 at 120iterations finished qdiffx linear iterations at : 15:35:39 total time elapsed so far: 8.800000 # loops : 120 mean,max change (kT/e) : 7.5968076E-04 2.4785995E-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 15:35:40 8.973u 0.437s 0:10.21 92.0% 0+0k 0+45392io 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 Wed Sep 30 2009 at 15:35:40 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3541 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 : 3541 total number of charged atoms : 3393 net assigned charge : 2.000013 assigned positive charge : 541.4822 centred at (gu) : 84.39677 79.92243 89.82726 assigned negative charge : -539.4841 centred at (gu) : 84.42178 79.66234 89.68089 start vw surface at 0.1700000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 202797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28533 grid for indexing accessible points = 1.400000 m= 99402 mr = 149893 m= 31762 mr = 81258 m= 6163 mr = 24934 m= 605 mr = 4494 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 1.820000 number of dielectric boundary points 79810 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 27134 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 -0.3007959 -5.8021218E-02 midg,1,midg; midg,igrid,midg -0.2627669 5.9723951E-02 1,midg,midg; igrid,midg,midg 0.3671205 0.3913028 gauss-seidel spectral radius is 0.9992429 estimated iterations to convergence 287 setup time was (sec) 2.130000 now iterating at: 15:35:42 rms-change max change #iterations 10.77507 306.5806 at 10iterations 6.256860 158.5306 at 20iterations 3.607415 68.25911 at 30iterations 2.077543 42.64185 at 40iterations 1.193014 23.49758 at 50iterations 0.6837419 12.69258 at 60iterations 0.3920699 8.484903 at 70iterations 0.2246382 4.178101 at 80iterations 0.1284447 2.508045 at 90iterations 7.3485218E-02 1.299431 at 100iterations 4.1907519E-02 0.7441845 at 110iterations 2.3988256E-02 0.4264247 at 120iterations 1.3720020E-02 0.2455773 at 130iterations 7.8461859E-03 0.1501846 at 140iterations 4.4855974E-03 8.1011772E-02 at 150iterations 2.5614267E-03 4.1915894E-02 at 160iterations 1.4682333E-03 2.4532318E-02 at 170iterations 8.4461150E-04 1.5140533E-02 at 180iterations finished qdiffx linear iterations at : 15:35:56 total time elapsed so far: 15.08000 # loops : 180 mean,max change (kT/e) : 8.4461150E-04 1.5140533E-02 energy calculations done at 15.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.26000 DelPhi exited at 15:35:57 15.261u 0.477s 0:16.72 94.0% 0+0k 0+45400io 0pf+0w