___________________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 Thu Sep 17 2009 at 13:10:30 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: 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 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7931 nv = 96 ne = 84 npr = 73074 no. pairs analyzed = 73074 no. exposed pairs = 3996 no. arc points = 27964 no. surface atoms = 1354 nbur = 2184 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= 354 mr = 4476 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 0.4100000 number of dielectric boundary points 3783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2892 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.5300000 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 0.9853643 estimated iterations to convergence 68 setup time was (sec) 0.6600000 now iterating at: 13:10:31 rms-change max change #iterations 0.1202539 17.58434 at 10iterations 1.0077440E-02 1.530177 at 20iterations 8.4350997E-04 0.1130342 at 30iterations 7.7319739E-05 9.7961426E-03 at 40iterations 9.6848535E-06 1.3141632E-03 at 50iterations finished qdiffx linear iterations at : 13:10:34 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 9.6848535E-06 1.3141632E-03 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 13:10:35 3.931u 0.359s 0:04.64 92.2% 0+0k 0+46072io 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 Thu Sep 17 2009 at 13:10:35 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 0.3100000 boundary points on vw surface= 88500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27964 grid for indexing accessible points = 1.400000 m= 29693 mr = 63218 m= 3720 mr = 21724 m= 137 mr = 2167 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 0.7200000 number of dielectric boundary points 34912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 253 iepsmp to db, and charging done at 0.8400000 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 -2.2080263E-02 -6.5010134E-03 midg,1,midg; midg,igrid,midg -5.2427547E-03 1.2515693E-02 1,midg,midg; igrid,midg,midg 2.9650740E-02 3.0619103E-02 gauss-seidel spectral radius is 0.9985194 estimated iterations to convergence 206 setup time was (sec) 1.000000 now iterating at: 13:10:36 rms-change max change #iterations 4.450539 152.0383 at 10iterations 2.021565 64.56004 at 20iterations 0.9158465 27.79272 at 30iterations 0.4171310 13.61538 at 40iterations 0.1894310 5.844500 at 50iterations 8.6063586E-02 2.442767 at 60iterations 3.9142169E-02 1.124401 at 70iterations 1.7794261E-02 0.6257877 at 80iterations 8.1076995E-03 0.2941628 at 90iterations 3.6797517E-03 0.1233082 at 100iterations 1.6727138E-03 4.9343109E-02 at 110iterations 7.6576992E-04 2.4744987E-02 at 120iterations finished qdiffx linear iterations at : 13:10:44 total time elapsed so far: 8.880000 # loops : 120 mean,max change (kT/e) : 7.6576992E-04 2.4744987E-02 energy calculations done at 8.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 13:10:45 9.049u 0.420s 0:10.03 94.3% 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 Thu Sep 17 2009 at 13:10:45 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= 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 : 2.000005 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 0.1700000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 205002 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27964 grid for indexing accessible points = 1.400000 m= 100310 mr = 152856 m= 31915 mr = 82463 m= 6225 mr = 25192 m= 611 mr = 4580 m= 7 mr = 349 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 78630 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 -0.2914099 -7.1418874E-02 midg,1,midg; midg,igrid,midg -0.2603807 6.2990271E-02 1,midg,midg; igrid,midg,midg 0.3697262 0.3963517 gauss-seidel spectral radius is 0.9992397 estimated iterations to convergence 286 setup time was (sec) 2.130000 now iterating at: 13:10:48 rms-change max change #iterations 10.69365 306.2339 at 10iterations 6.174654 127.9832 at 20iterations 3.548152 69.89565 at 30iterations 2.036997 43.99757 at 40iterations 1.166307 22.53251 at 50iterations 0.6674277 12.62797 at 60iterations 0.3816028 7.093180 at 70iterations 0.2184223 3.865467 at 80iterations 0.1247232 2.039968 at 90iterations 7.1229972E-02 1.282768 at 100iterations 4.0621396E-02 0.7559519 at 110iterations 2.3209689E-02 0.4305933 at 120iterations 1.3273098E-02 0.2474432 at 130iterations 7.5775515E-03 0.1283903 at 140iterations 4.3343296E-03 7.4559212E-02 at 150iterations 2.4732545E-03 4.1846752E-02 at 160iterations 1.4176083E-03 2.7790070E-02 at 170iterations 8.1853598E-04 1.3618469E-02 at 180iterations finished qdiffx linear iterations at : 13:11:01 total time elapsed so far: 15.16000 # loops : 180 mean,max change (kT/e) : 8.1853598E-04 1.3618469E-02 energy calculations done at 15.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.32000 DelPhi exited at 13:11:01 15.326u 0.447s 0:16.36 96.3% 0+0k 0+45392io 0pf+0w