-
Notifications
You must be signed in to change notification settings - Fork 0
/
packmol.out
151 lines (102 loc) · 5.9 KB
/
packmol.out
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
################################################################################
PACKMOL - Packing optimization for the automated generation of
starting configurations for molecular dynamics simulations.
Version 20.010
################################################################################
Packmol must be run with: packmol < inputfile.inp
Userguide at: http://m3g.iqm.unicamp.br/packmol
Reading input file... (Control-C aborts)
Seed for random number generator: 1234567
Output file: box.pdb
Reading coordinate file: water.pdb
Number of independent structures: 1
The structures are:
Structure 1 :water.pdb( 3 atoms)
Maximum number of GENCAN loops for all molecule packing: 200
Total number of restrictions: 1
Distance tolerance: 2.0000000000000000
Warning: Type of residue numbering not set for structure 1
Residue numbering set for structure 1 : 0
Swap chains of molecules of structure 1 : F
Number of molecules of type 1 : 1000
Total number of atoms: 3000
Total number of molecules: 1000
Number of fixed molecules: 0
Number of free molecules: 1000
Number of variables: 6000
Total number of fixed atoms: 0
Maximum internal distance of type 1 : 1.6330000000000000
All atoms must be within these coordinates:
x: [ -999.24636734693877 , 1000.7536326530612 ]
y: [ -998.39999999999998 , 1001.6000000000000 ]
z: [ -1000.0000000000000 , 1000.0000000000000 ]
If the system is larger than this, increase the sidemax parameter.
################################################################################
Building initial approximation ...
################################################################################
Adjusting initial point to fit the constraints
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Molecules of type: 1
Packing:|0 100%|
|****************************
Restraint-only function value: 2.0616067554899503E-002
Maximum violation of the restraints: 1.9769379682143522E-003
--------------------------------------------------------------------------------
Rescaling maximum and minimum coordinates...
Computing size of patches...
Add fixed molecules to permanent arrays...
Reseting center of mass...
--------------------------------------------------------------------------------
Setting initial trial coordinates ...
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Molecules of type: 1
Adjusting random positions to fit the constraints.
Packing:|0 100%|
|*******
Restraint-only function value: 1.0752447321139317E-005
Maximum violation of the restraints: 4.5820839623406773E-006
################################################################################
Objective function at initial point: 17421.541519772367
################################################################################
Packing molecules of type: 1
################################################################################
--------------------------------------------------------------------------------
Starting GENCAN loop: 0
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|******************************************************************|
|******************************************
Function value from last GENCAN loop: f = .37323E-01
Best function value before: f = .17422E+05
Improvement from best function value: 99.99 %
Improvement from last loop: 99.99 %
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .69488E-02
Current structure written to file: box.pdb
--------------------------------------------------------------------------------
Packing solved for molecules of type 1
Objective function value: 3.7323329723344748E-002
Maximum violation of target distance: 0.0000000000000000
Max. constraint violation: 6.9487744272116493E-003
--------------------------------------------------------------------------------
################################################################################
Packing all molecules together
################################################################################
Initial approximation is a solution. Nothing to do.
Solution written to file: box.pdb
################################################################################
Success!
Final objective function value: .24268E+01
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .69488E-02
--------------------------------------------------------------------------------
Please cite this work if Packmol was useful:
L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez,
PACKMOL: A package for building initial configurations for
molecular dynamics simulations.
Journal of Computational Chemistry, 30:2157-2164,2009.
################################################################################
Running time: 0.352849990 seconds.
--------------------------------------------------------------------------------