___________________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 09:19:52 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: 285 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 : 2.000013 assigned positive charge : 540.9802 centred at (gu) : 88.74609 87.75481 89.95493 assigned negative charge : -538.9821 centred at (gu) : 88.75138 87.69746 89.92338 start vw surface at 0.1600000 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 0.5300000 number of grid points assigned charge 10278 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5649341E-10 1.9946849E-09 midg,1,midg; midg,igrid,midg -2.7732390E-09 1.8311598E-09 1,midg,midg; igrid,midg,midg 1.2655340E-09 3.9795056E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6600000 now iterating at: 09:19:53 rms-change max change #iterations 0.1189589 17.59689 at 10iterations 9.9590868E-03 1.441158 at 20iterations 8.3390914E-04 0.1194944 at 30iterations 7.1769384E-05 9.8934174E-03 at 40iterations 7.1582231E-06 1.0070801E-03 at 50iterations finished qdiffx linear iterations at : 09:19:56 total time elapsed so far: 3.810000 # loops : 50 mean,max change (kT/e) : 7.1582231E-06 1.0070801E-03 energy calculations done at 3.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.960000 DelPhi exited at 09:19:57 3.964u 0.384s 0:05.26 82.5% 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 09:19:57 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: 285 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 : 540.9802 centred at (gu) : 86.23761 83.26358 89.86406 assigned negative charge : -538.9821 centred at (gu) : 86.25382 83.09192 89.76996 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 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 = 0.3400000 no. cavity mid-points inaccessible to solvent = 2330 time to turn everything in is 0.7200000 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 0.8500000 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 -2.2071840E-02 -5.0760875E-03 midg,1,midg; midg,igrid,midg -5.5120401E-03 1.1827995E-02 1,midg,midg; igrid,midg,midg 2.9361064E-02 2.9900778E-02 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 1.000000 now iterating at: 09:19:58 rms-change max change #iterations 4.451463 159.8083 at 10iterations 2.022976 65.03341 at 20iterations 0.9148091 27.82944 at 30iterations 0.4174771 12.81920 at 40iterations 0.1889810 5.863787 at 50iterations 8.5921958E-02 2.528238 at 60iterations 3.8988348E-02 1.164505 at 70iterations 1.7719474E-02 0.6630898 at 80iterations 8.0543356E-03 0.2592659 at 90iterations 3.6621187E-03 0.1310253 at 100iterations 1.6656022E-03 5.1586151E-02 at 110iterations 7.5988314E-04 2.5311470E-02 at 120iterations finished qdiffx linear iterations at : 09:20:06 total time elapsed so far: 8.930000 # loops : 120 mean,max change (kT/e) : 7.5988314E-04 2.5311470E-02 energy calculations done at 8.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.070000 DelPhi exited at 09:20:07 9.071u 0.420s 0:10.18 93.2% 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 09:20:07 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: 285 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 : 540.9802 centred at (gu) : 84.35613 79.89502 89.79591 assigned negative charge : -538.9821 centred at (gu) : 84.38074 79.63772 89.65469 start vw surface at 0.1800000 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 1.820000 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 1.970000 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 -0.2913778 -5.8371380E-02 midg,1,midg; midg,igrid,midg -0.2644425 5.4228321E-02 1,midg,midg; igrid,midg,midg 0.3651286 0.3886145 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 2.130000 now iterating at: 09:20:09 rms-change max change #iterations 10.78199 306.6192 at 10iterations 6.261641 160.4609 at 20iterations 3.610172 70.81435 at 30iterations 2.080176 40.57158 at 40iterations 1.194035 22.80720 at 50iterations 0.6846007 14.13335 at 60iterations 0.3926359 7.535490 at 70iterations 0.2249846 3.856316 at 80iterations 0.1286337 2.137805 at 90iterations 7.3552705E-02 1.288734 at 100iterations 4.1988596E-02 0.7691135 at 110iterations 2.4032649E-02 0.4315631 at 120iterations 1.3742239E-02 0.2433796 at 130iterations 7.8646904E-03 0.1580162 at 140iterations 4.4961474E-03 8.2260132E-02 at 150iterations 2.5676345E-03 4.5375109E-02 at 160iterations 1.4717962E-03 2.3923874E-02 at 170iterations 8.4728090E-04 1.6515732E-02 at 180iterations finished qdiffx linear iterations at : 09:20:23 total time elapsed so far: 15.27000 # loops : 180 mean,max change (kT/e) : 8.4728090E-04 1.6515732E-02 energy calculations done at 15.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.43000 DelPhi exited at 09:20:24 15.439u 0.422s 0:16.62 95.3% 0+0k 0+45392io 0pf+0w