___________________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 Sep 29 2009 at 19:09:24 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 = 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 : 2.000013 assigned positive charge : 540.6483 centred at (gu) : 88.74480 87.75479 89.96137 assigned negative charge : -538.6500 centred at (gu) : 88.74999 87.69688 89.92982 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7868 nv = 96 ne = 84 npr = 74698 no. pairs analyzed = 74698 no. exposed pairs = 4093 no. arc points = 28513 no. surface atoms = 1383 nbur = 2155 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 = 4359 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 0.4200000 number of dielectric boundary points 3837 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2969 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10277 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5425387E-10 1.9973792E-09 midg,1,midg; midg,igrid,midg -2.8093243E-09 1.8441787E-09 1,midg,midg; igrid,midg,midg 1.2614695E-09 4.0113882E-10 gauss-seidel spectral radius is 0.9853630 estimated iterations to convergence 68 setup time was (sec) 0.6900000 now iterating at: 19:09:26 rms-change max change #iterations 0.1197544 17.59708 at 10iterations 1.0019465E-02 1.451126 at 20iterations 8.3639222E-04 0.1198425 at 30iterations 7.0600836E-05 9.5930099E-03 at 40iterations 6.5783875E-06 9.0408325E-04 at 50iterations finished qdiffx linear iterations at : 19:09:29 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 6.5783875E-06 9.0408325E-04 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 19:09:30 3.935u 0.345s 0:06.02 70.9% 0+0k 48+46080io 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 Sep 29 2009 at 19:09:31 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: 282 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 : 2.000013 assigned positive charge : 540.6483 centred at (gu) : 86.23376 83.26357 89.88341 assigned negative charge : -538.6500 centred at (gu) : 86.24963 83.09019 89.78931 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 87506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28513 grid for indexing accessible points = 1.400000 m= 29472 mr = 61860 m= 3712 mr = 21395 m= 141 mr = 2131 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 0.7400000 number of dielectric boundary points 35416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 258 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 26405 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 -2.2664001E-02 -5.6179748E-03 midg,1,midg; midg,igrid,midg -5.4545645E-03 1.2181921E-02 1,midg,midg; igrid,midg,midg 2.9411798E-02 3.0479630E-02 gauss-seidel spectral radius is 0.9985187 estimated iterations to convergence 206 setup time was (sec) 1.030000 now iterating at: 19:09:32 rms-change max change #iterations 4.450124 152.0131 at 10iterations 2.020322 66.62712 at 20iterations 0.9140244 27.82612 at 30iterations 0.4164233 12.65406 at 40iterations 0.1887177 5.797599 at 50iterations 8.5796848E-02 2.651150 at 60iterations 3.8914874E-02 1.133385 at 70iterations 1.7708354E-02 0.6389027 at 80iterations 8.0512473E-03 0.2543678 at 90iterations 3.6582944E-03 0.1204796 at 100iterations 1.6622855E-03 5.0815582E-02 at 110iterations 7.5919263E-04 2.4839401E-02 at 120iterations finished qdiffx linear iterations at : 19:09:40 total time elapsed so far: 8.850000 # loops : 120 mean,max change (kT/e) : 7.5919263E-04 2.4839401E-02 energy calculations done at 8.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.030000 DelPhi exited at 19:09:41 9.030u 0.389s 0:10.71 87.8% 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 Sep 29 2009 at 19:09:41 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 = 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: 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 : 2.000013 assigned positive charge : 540.6483 centred at (gu) : 84.35035 79.89502 89.82493 assigned negative charge : -538.6500 centred at (gu) : 84.37444 79.63511 89.68372 start vw surface at 0.1700000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 202637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28513 grid for indexing accessible points = 1.400000 m= 99273 mr = 149839 m= 31732 mr = 81090 m= 6188 mr = 24914 m= 608 mr = 4506 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 1.810000 number of dielectric boundary points 79749 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 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 -0.2991879 -6.3908890E-02 midg,1,midg; midg,igrid,midg -0.2632970 5.8892116E-02 1,midg,midg; igrid,midg,midg 0.3663310 0.3975219 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 2.120000 now iterating at: 19:09:44 rms-change max change #iterations 10.76507 306.4906 at 10iterations 6.248198 137.6754 at 20iterations 3.606383 69.00204 at 30iterations 2.077202 43.43607 at 40iterations 1.191991 22.91132 at 50iterations 0.6839777 13.81094 at 60iterations 0.3922465 8.060595 at 70iterations 0.2247056 4.076900 at 80iterations 0.1284932 2.268988 at 90iterations 7.3480316E-02 1.337376 at 100iterations 4.1951973E-02 0.7370834 at 110iterations 2.3993727E-02 0.4125671 at 120iterations 1.3730313E-02 0.2380986 at 130iterations 7.8520542E-03 0.1363220 at 140iterations 4.4890749E-03 7.6115608E-02 at 150iterations 2.5608502E-03 4.6752930E-02 at 160iterations 1.4680085E-03 2.6782990E-02 at 170iterations 8.4481813E-04 1.5738010E-02 at 180iterations finished qdiffx linear iterations at : 19:09:57 total time elapsed so far: 15.06000 # loops : 180 mean,max change (kT/e) : 8.4481813E-04 1.5738010E-02 energy calculations done at 15.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.24000 DelPhi exited at 19:09:58 15.245u 0.470s 0:16.84 93.2% 0+0k 0+45392io 0pf+0w