___________________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 11:51:16 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: 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: 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 : 538.6483 centred at (gu) : 88.73242 87.74290 89.95646 assigned negative charge : -536.6500 centred at (gu) : 88.74094 87.68509 89.92440 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 = 0.2000000 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 = 4476 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 0.4000000 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 0.5100000 number of grid points assigned charge 10279 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7289046E-10 2.0088526E-09 midg,1,midg; midg,igrid,midg -2.7978053E-09 1.8303659E-09 1,midg,midg; igrid,midg,midg 1.4425710E-09 2.9871555E-10 gauss-seidel spectral radius is 0.9853643 estimated iterations to convergence 68 setup time was (sec) 0.6500000 now iterating at: 11:51:17 rms-change max change #iterations 0.1191906 17.58434 at 10iterations 1.0004107E-02 1.459044 at 20iterations 8.4269908E-04 0.1141167 at 30iterations 8.1598257E-05 9.7675323E-03 at 40iterations 1.1811700E-05 1.4877319E-03 at 50iterations finished qdiffx linear iterations at : 11:51:20 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 1.1811700E-05 1.4877319E-03 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 11:51:21 3.912u 0.392s 0:05.29 81.2% 0+0k 16+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 11:51:21 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: 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 : 538.6483 centred at (gu) : 86.19659 83.22789 89.86866 assigned negative charge : -536.6500 centred at (gu) : 86.22243 83.05479 89.77293 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 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 0.7300000 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 0.8600000 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 -2.2086646E-02 -6.3442946E-03 midg,1,midg; midg,igrid,midg -5.0867763E-03 1.2431244E-02 1,midg,midg; igrid,midg,midg 3.0092185E-02 3.0369015E-02 gauss-seidel spectral radius is 0.9985194 estimated iterations to convergence 206 setup time was (sec) 1.010000 now iterating at: 11:51:22 rms-change max change #iterations 4.430017 152.0383 at 10iterations 2.011715 64.56004 at 20iterations 0.9114986 27.77267 at 30iterations 0.4152621 13.39073 at 40iterations 0.1885426 5.838401 at 50iterations 8.5669681E-02 2.480995 at 60iterations 3.8962416E-02 1.115738 at 70iterations 1.7710051E-02 0.6229877 at 80iterations 8.0717774E-03 0.2918968 at 90iterations 3.6635448E-03 0.1216316 at 100iterations 1.6659165E-03 4.9545288E-02 at 110iterations 7.6312805E-04 2.4578094E-02 at 120iterations finished qdiffx linear iterations at : 11:51:31 total time elapsed so far: 8.840000 # loops : 120 mean,max change (kT/e) : 7.6312805E-04 2.4578094E-02 energy calculations done at 8.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.010000 DelPhi exited at 11:51:31 9.016u 0.392s 0:10.55 89.0% 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 11:51:32 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: 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 : 538.6483 centred at (gu) : 84.29462 79.84150 89.80281 assigned negative charge : -536.6500 centred at (gu) : 84.33363 79.58204 89.65913 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 1.990000 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 -0.2914651 -6.9535635E-02 midg,1,midg; midg,igrid,midg -0.2584210 6.1970934E-02 1,midg,midg; igrid,midg,midg 0.3754172 0.3931211 gauss-seidel spectral radius is 0.9992397 estimated iterations to convergence 286 setup time was (sec) 2.150000 now iterating at: 11:51:34 rms-change max change #iterations 10.65038 306.2338 at 10iterations 6.151868 127.9797 at 20iterations 3.534973 67.23662 at 30iterations 2.029491 42.49944 at 40iterations 1.162124 22.43745 at 50iterations 0.6650147 12.49186 at 60iterations 0.3802494 6.978848 at 70iterations 0.2176955 3.789734 at 80iterations 0.1243075 2.038032 at 90iterations 7.0996493E-02 1.277234 at 100iterations 4.0490918E-02 0.7410866 at 110iterations 2.3137821E-02 0.4325595 at 120iterations 1.3234219E-02 0.2484174 at 130iterations 7.5586485E-03 0.1312542 at 140iterations 4.3255114E-03 7.4685097E-02 at 150iterations 2.4702700E-03 4.1706085E-02 at 160iterations 1.4182599E-03 2.7973175E-02 at 170iterations 8.2092866E-04 1.3700485E-02 at 180iterations finished qdiffx linear iterations at : 11:51:47 total time elapsed so far: 15.11000 # loops : 180 mean,max change (kT/e) : 8.2092866E-04 1.3700485E-02 energy calculations done at 15.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.28000 DelPhi exited at 11:51:48 15.282u 0.401s 0:16.72 93.7% 0+0k 0+45392io 0pf+0w