___________________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 Mon May 16 2011 at 12:47:20 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: 290 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 : 2.000014 assigned positive charge : 541.7802 centred at (gu) : 88.75487 87.75731 89.95785 assigned negative charge : -539.7820 centred at (gu) : 88.76093 87.70016 89.92683 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7880 nv = 96 ne = 84 npr = 75514 no. pairs analyzed = 75514 no. exposed pairs = 4085 no. arc points = 28552 no. surface atoms = 1382 nbur = 2156 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= 353 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= 2978 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10278 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3649174E-10 1.9759869E-09 midg,1,midg; midg,igrid,midg -2.7641762E-09 1.8291015E-09 1,midg,midg; igrid,midg,midg 1.3050413E-09 3.7420905E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6600000 now iterating at: 12:47:21 rms-change max change #iterations 0.1194008 17.59689 at 10iterations 9.9861817E-03 1.449841 at 20iterations 8.3706639E-04 0.1192026 at 30iterations 7.2601906E-05 9.9163055E-03 at 40iterations 7.5094963E-06 1.0604858E-03 at 50iterations finished qdiffx linear iterations at : 12:47:24 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 7.5094963E-06 1.0604858E-03 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 12:47:25 3.880u 0.426s 0:04.78 89.9% 0+0k 0+46088io 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 Mon May 16 2011 at 12:47:25 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: 290 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 : 2.000014 assigned positive charge : 541.7802 centred at (gu) : 86.26398 83.27109 89.87283 assigned negative charge : -539.7820 centred at (gu) : 86.28247 83.10005 89.78033 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 87602 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28552 grid for indexing accessible points = 1.400000 m= 29515 mr = 61879 m= 3712 mr = 21454 m= 139 mr = 2125 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 35481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 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 -2.1939103E-02 -5.1199286E-03 midg,1,midg; midg,igrid,midg -5.4457281E-03 1.1840330E-02 1,midg,midg; igrid,midg,midg 2.9412949E-02 2.9691746E-02 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 0.9900000 now iterating at: 12:47:26 rms-change max change #iterations 4.460273 159.4774 at 10iterations 2.026624 65.03341 at 20iterations 0.9164752 27.89269 at 30iterations 0.4182237 12.61078 at 40iterations 0.1893321 5.845099 at 50iterations 8.6082086E-02 2.528241 at 60iterations 3.9053917E-02 1.178452 at 70iterations 1.7752130E-02 0.6711521 at 80iterations 8.0686212E-03 0.2580338 at 90iterations 3.6685751E-03 0.1313725 at 100iterations 1.6689165E-03 5.1357269E-02 at 110iterations 7.6132186E-04 2.5570869E-02 at 120iterations finished qdiffx linear iterations at : 12:47:34 total time elapsed so far: 8.860000 # loops : 120 mean,max change (kT/e) : 7.6132186E-04 2.5570869E-02 energy calculations done at 8.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.980000 DelPhi exited at 12:47:35 8.982u 0.490s 0:09.87 95.9% 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 Mon May 16 2011 at 12:47:35 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: 290 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 : 2.000014 assigned positive charge : 541.7802 centred at (gu) : 84.39569 79.90629 89.80907 assigned negative charge : -539.7820 centred at (gu) : 84.42370 79.64990 89.67024 start vw surface at 0.1700000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 202796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28552 grid for indexing accessible points = 1.400000 m= 99417 mr = 149838 m= 31759 mr = 81234 m= 6154 mr = 24945 m= 604 mr = 4496 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 1.800000 number of dielectric boundary points 79877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.950000 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 -0.2897214 -5.8904294E-02 midg,1,midg; midg,igrid,midg -0.2635130 5.4390062E-02 1,midg,midg; igrid,midg,midg 0.3657863 0.3850189 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 2.110000 now iterating at: 12:47:37 rms-change max change #iterations 10.80027 306.6192 at 10iterations 6.271971 161.1850 at 20iterations 3.615791 72.02159 at 30iterations 2.083485 40.42919 at 40iterations 1.195898 22.59552 at 50iterations 0.6856641 14.12340 at 60iterations 0.3932401 7.628618 at 70iterations 0.2253125 3.879293 at 80iterations 0.1288182 2.157114 at 90iterations 7.3655002E-02 1.276596 at 100iterations 4.2050507E-02 0.7693977 at 110iterations 2.4067691E-02 0.4311197 at 120iterations 1.3761922E-02 0.2447519 at 130iterations 7.8762043E-03 0.1575470 at 140iterations 4.5030429E-03 8.1890106E-02 at 150iterations 2.5717348E-03 4.5500040E-02 at 160iterations 1.4744176E-03 2.4051666E-02 at 170iterations 8.4906485E-04 1.6410828E-02 at 180iterations finished qdiffx linear iterations at : 12:47:51 total time elapsed so far: 15.58000 # loops : 180 mean,max change (kT/e) : 8.4906485E-04 1.6410828E-02 energy calculations done at 15.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.73000 DelPhi exited at 12:47:52 15.736u 0.467s 0:17.11 94.6% 0+0k 0+45392io 0pf+0w