1debug: Input string:
2read
3 mol pqr ion.pqr
4end
5
6elec name elec
7mg-manual
8dime 33 33 33
9grid 0.500 0.500 0.500
10# nlev 4
11gcent mol 1
12ion charge 1.000 conc 0.150 radius 2.000
13ion charge -1.000 conc 0.150 radius 2.000
14pdie 2.000
15sdie 78.540
16srad 1.400
17swin 0.300
18temp 298.150
19sdens 10.000
20mol 1
21chgm spl2
22lpbe
23bcfl sdh
24srfm spl2
25calcenergy total
26calcforce total
27end
28
29apolar name npolar
30bconc 0.0
31press 0.0
32dpos 0.2
33mol 1
34srfm sacc
35grid 0.2 0.2 0.2
36gamma 0.105
37srad 1.400
38swin 0.300
39temp 298.150
40sdens 10.000
41calcenergy total
42calcforce comps
43end
44
45
46quit
47
48Parsed input string.
49Preparing to run 2 PBE calculations.
50----------------------------------------
51CALCULATION #1 (elec): MULTIGRID
52  Setting up problem...
53  Using cubic spline charge discretization.
54  Grid dimensions: 33 x 33 x 33
55  Grid spacings: 0.500 x 0.500 x 0.500
56  Grid lengths: 16.000 x 16.000 x 16.000
57  Grid center: (4.681, 3.930, -0.620)
58  Multigrid levels: 4
59  Molecule ID: 1
60  Linearized traditional PBE
61  Single Debye-Huckel sphere boundary conditions
62  2 ion species (0.150 M ionic strength):
63    2.000 A-radius, 1.000 e-charge, 0.150 M concentration
64    2.000 A-radius, -1.000 e-charge, 0.150 M concentration
65  Solute dielectric: 2.000
66  Solvent dielectric: 78.540
67  Using spline-based surface definition;window = 0.300
68  Temperature:  298.150 K
69  Electrostatic energies will be calculated
70  Net solvent forces will be calculated
71----------------------------------------
72CALCULATION #2 (npolar): APOLAR
73----------------------------------------
74Final memory usage:  0.001 MB total, 8.547 MB high water
75Reading parameter file apbs-forces-tot.in
76 Reading PQR file ...
77Mol. dimensions:    6.386   4.868   5.895
78 Grid dime not specified, calculating ...
79 Grid values:
80fglen:   26.386  24.868  25.895
81cglen:   26.386  24.868  25.895
82dime:   33  33  33
83grid:    0.500   0.500   0.500
84Required memory (in MB):      6.854
85 PQR file (x, y, z, charge, radius):
86   1   3.555   3.970  -0.000  -0.416   1.824
87   2   2.733   4.556  -0.000   0.272   0.600
88   3   4.853   4.614  -0.000   0.034   1.908
89   4   5.408   4.316   0.890   0.082   1.387
90   5   5.661   4.221  -1.232  -0.182   1.908
91   6   5.123   4.521  -2.131   0.060   1.487
92   7   6.630   4.719  -1.206   0.060   1.487
93   8   5.809   3.141  -1.241   0.060   1.487
94 i_param:
95calc_type   0
96nlev   4
97cmeth   1
98ccmeth   1
99fcmeth   1
100chgm   1
101nonlin   0
102bcfl   1
103srfm   2
104calcenergy   1
105calcforce   1
106wpot   0
107wchg   0
108wsmol   0
109wkappa   0
110wdiel   0
111watompot   0
112rpot   0
1130   0
114calcnpforce   2
115calcnpenergy   1
116nion   2
117rchg   0
118rkappa   0
119rdiel   0
120 r_param:
121pdie   2.000
122 main.f: apbs return code:            0
123esenergy (kJ/mol):   150.87575187
124npenergy (kJ/mol):    22.80602401
125esenergy (kcal/mol):    36.06017001
126npenergy (kcal/mol):     5.45077054
127 main: Total force on molecule kJ/(mol/A)
128qf    -58.07701165   40.45922947   57.50773299
129ib      0.00014582    0.00025737   -0.00002647
130db      9.74780014   -2.44894324   -1.03462148
131pol   -48.32906569   38.01054360   56.47308504
132apol   43.94102579   24.67825906  -15.48817878
133tot    -4.38803990   62.68880266   40.98490626
134