___________________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 20:56:20 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= 7883 nv = 96 ne = 84 npr = 75649 no. pairs analyzed = 75649 no. exposed pairs = 4092 no. arc points = 28588 no. surface atoms = 1381 nbur = 2157 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= 355 mr = 4368 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 0.4300000 number of dielectric boundary points 3844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2981 ## 358 charges are in solution ## iepsmp to db, and charging done at 0.5600000 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 0.9853627 estimated iterations to convergence 68 setup time was (sec) 0.7000000 now iterating at: 20:56:21 rms-change max change #iterations 0.1198294 17.59671 at 10iterations 9.9868672E-03 1.452991 at 20iterations 8.3327119E-04 0.1171637 at 30iterations 7.0159920E-05 9.3641281E-03 at 40iterations 6.4287565E-06 8.9263916E-04 at 50iterations finished qdiffx linear iterations at : 20:56:25 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 6.4287565E-06 8.9263916E-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) 3.950000 DelPhi exited at 20:56:25 3.957u 0.373s 0:05.31 81.3% 0+0k 600+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 Sep 29 2009 at 20:56:26 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 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 87582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28588 grid for indexing accessible points = 1.400000 m= 29499 mr = 61861 m= 3700 mr = 21410 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 0.7200000 number of dielectric boundary points 35494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 iepsmp to db, and charging done at 0.8600000 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 -2.2701222E-02 -5.3080460E-03 midg,1,midg; midg,igrid,midg -5.4396796E-03 1.2155983E-02 1,midg,midg; igrid,midg,midg 2.9408047E-02 3.0273167E-02 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 1.010000 now iterating at: 20:56:27 rms-change max change #iterations 4.448444 152.0200 at 10iterations 2.020524 64.98824 at 20iterations 0.9132948 27.78407 at 30iterations 0.4165844 12.60947 at 40iterations 0.1887283 5.830830 at 50iterations 8.5813917E-02 2.865227 at 60iterations 3.8967714E-02 1.119705 at 70iterations 1.7678311E-02 0.6342754 at 80iterations 8.0412356E-03 0.2552309 at 90iterations 3.6541838E-03 0.1323853 at 100iterations 1.6612549E-03 5.2818298E-02 at 110iterations 7.5796305E-04 2.3812294E-02 at 120iterations finished qdiffx linear iterations at : 20:56:36 total time elapsed so far: 8.960000 # loops : 120 mean,max change (kT/e) : 7.5796305E-04 2.3812294E-02 energy calculations done at 8.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.130000 DelPhi exited at 20:56:37 9.137u 0.403s 0:11.03 86.4% 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 20:56:37 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= 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 : 2.000013 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 0.1600000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 202747 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28588 grid for indexing accessible points = 1.400000 m= 99357 mr = 149790 m= 31717 mr = 81147 m= 6144 mr = 24891 m= 604 mr = 4491 m= 7 mr = 347 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 8260 time to turn everything in is 1.820000 number of dielectric boundary points 79910 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 -0.2996564 -6.1274879E-02 midg,1,midg; midg,igrid,midg -0.2634332 5.9139725E-02 1,midg,midg; igrid,midg,midg 0.3661940 0.3929674 gauss-seidel spectral radius is 0.9992434 estimated iterations to convergence 287 setup time was (sec) 2.130000 now iterating at: 20:56:39 rms-change max change #iterations 10.76309 306.6319 at 10iterations 6.248998 151.0901 at 20iterations 3.603662 70.43170 at 30iterations 2.076514 43.50490 at 40iterations 1.192023 22.16770 at 50iterations 0.6834463 12.89739 at 60iterations 0.3919353 8.557966 at 70iterations 0.2245381 4.115730 at 80iterations 0.1284492 2.384563 at 90iterations 7.3495723E-02 1.299812 at 100iterations 4.1939098E-02 0.7192268 at 110iterations 2.4004193E-02 0.4191258 at 120iterations 1.3728013E-02 0.2501740 at 130iterations 7.8555727E-03 0.1502075 at 140iterations 4.4878297E-03 7.7139378E-02 at 150iterations 2.5634104E-03 4.3301344E-02 at 160iterations 1.4694521E-03 2.4996281E-02 at 170iterations 8.4525498E-04 1.5844345E-02 at 180iterations finished qdiffx linear iterations at : 20:56:53 total time elapsed so far: 15.08000 # loops : 180 mean,max change (kT/e) : 8.4525498E-04 1.5844345E-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) 15.24000 DelPhi exited at 20:56:54 15.247u 0.470s 0:16.84 93.2% 0+0k 0+45392io 0pf+0w