___________________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 Fri May 13 2011 at 13:33:47 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: 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 : 541.1802 centred at (gu) : 88.74754 87.75494 89.95750 assigned negative charge : -539.1821 centred at (gu) : 88.75349 87.69767 89.92641 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 0.4200000 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 0.5400000 number of grid points assigned charge 10278 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3844079E-10 1.9779378E-09 midg,1,midg; midg,igrid,midg -2.7695477E-09 1.8294058E-09 1,midg,midg; igrid,midg,midg 1.3013115E-09 3.7720044E-10 gauss-seidel spectral radius is 0.9853628 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 13:33:48 rms-change max change #iterations 0.1193558 17.59689 at 10iterations 9.9716280E-03 1.449440 at 20iterations 8.3632860E-04 0.1198196 at 30iterations 7.2365001E-05 9.8018646E-03 at 40iterations 7.4426289E-06 1.0643005E-03 at 50iterations finished qdiffx linear iterations at : 13:33:51 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 7.4426289E-06 1.0643005E-03 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 13:33:52 3.874u 0.397s 0:04.87 87.4% 0+0k 608+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 Fri May 13 2011 at 13:33:52 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= 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 : 541.1802 centred at (gu) : 86.24200 83.26398 89.87180 assigned negative charge : -539.1821 centred at (gu) : 86.26015 83.09258 89.77905 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 -2.1996064E-02 -5.1353853E-03 midg,1,midg; midg,igrid,midg -5.4443129E-03 1.1851040E-02 1,midg,midg; igrid,midg,midg 2.9427880E-02 2.9807307E-02 gauss-seidel spectral radius is 0.9985189 estimated iterations to convergence 206 setup time was (sec) 0.9900000 now iterating at: 13:33:53 rms-change max change #iterations 4.452839 152.0224 at 10iterations 2.023715 65.03342 at 20iterations 0.9149398 27.68809 at 30iterations 0.4174870 12.62994 at 40iterations 0.1890090 5.849161 at 50iterations 8.5940555E-02 2.510371 at 60iterations 3.8994834E-02 1.163643 at 70iterations 1.7722456E-02 0.6654778 at 80iterations 8.0548730E-03 0.2535095 at 90iterations 3.6633946E-03 0.1327343 at 100iterations 1.6661059E-03 5.2692413E-02 at 110iterations 7.5998047E-04 2.5247574E-02 at 120iterations finished qdiffx linear iterations at : 13:34:01 total time elapsed so far: 8.890000 # loops : 120 mean,max change (kT/e) : 7.5998047E-04 2.5247574E-02 energy calculations done at 8.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.020000 DelPhi exited at 13:34:02 9.027u 0.429s 0:09.90 95.3% 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 Fri May 13 2011 at 13:34:02 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: 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 : 541.1802 centred at (gu) : 84.36272 79.89564 89.80753 assigned negative charge : -539.1821 centred at (gu) : 84.39024 79.63871 89.66833 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 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 -0.2904685 -5.9077051E-02 midg,1,midg; midg,igrid,midg -0.2634821 5.4572284E-02 1,midg,midg; igrid,midg,midg 0.3660040 0.3873203 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 2.110000 now iterating at: 13:34:04 rms-change max change #iterations 10.78414 306.6192 at 10iterations 6.262341 160.4541 at 20iterations 3.610386 71.17812 at 30iterations 2.080239 40.53085 at 40iterations 1.194159 23.16569 at 50iterations 0.6846291 14.41706 at 60iterations 0.3926818 7.564198 at 70iterations 0.2250016 3.854399 at 80iterations 0.1286450 2.127378 at 90iterations 7.3560014E-02 1.275764 at 100iterations 4.1993931E-02 0.7699280 at 110iterations 2.4035212E-02 0.4300218 at 120iterations 1.3743117E-02 0.2428517 at 130iterations 7.8655956E-03 0.1564636 at 140iterations 4.4969884E-03 8.0591202E-02 at 150iterations 2.5682414E-03 4.5418024E-02 at 160iterations 1.4724708E-03 2.4215698E-02 at 170iterations 8.4796874E-04 1.6475677E-02 at 180iterations finished qdiffx linear iterations at : 13:34:17 total time elapsed so far: 15.23000 # loops : 180 mean,max change (kT/e) : 8.4796874E-04 1.6475677E-02 energy calculations done at 15.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.35000 DelPhi exited at 13:34:18 15.353u 0.472s 0:16.35 96.7% 0+0k 0+45392io 0pf+0w