A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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PACKMOL - Packing optimization for the automated generation of
starting configurations for molecular dynamics simulations.
Version 18.169
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Packmol must be run with: packmol < inputfile.inp
Userguide at: www.ime.unicamp.br/~martinez/packmol
Reading input file... (Control-C aborts)
Seed for random number generator: 1234567
Output file: system_init.pdb
Reading coordinate file: ../water/water_gaff.pdb
Reading coordinate file: ../urea/URA_gaff.pdb
Number of independent structures: 2
The structures are:
Structure 1 :../water/water_gaff.pdb( 3 atoms)
Structure 2 :../urea/URA_gaff.pdb( 8 atoms)
Maximum number of GENCAN loops for all molecule packing: 400
Total number of restrictions: 2
Distance tolerance: 2.5000000000000000
Residue numbering set for structure 1 : 3
Swap chains of molecules of structure 1 : F
Residue numbering set for structure 2 : 3
Swap chains of molecules of structure 2 : F
Number of molecules of type 1 : 100
Number of molecules of type 2 : 13
Total number of atoms: 404
Total number of molecules: 113
Number of fixed molecules: 0
Number of free molecules: 113
Number of variables: 678
Total number of fixed atoms: 0
Maximum internal distance of type 1 : 1.5444600998407179
Maximum internal distance of type 2 : 4.0422680514780316
All atoms must be within these coordinates:
x: [ -1000.0000000000000 , 1000.0000000000000 ]
y: [ -1000.0000000000000 , 1000.0000000000000 ]
z: [ -1000.0000000000000 , 1000.0000000000000 ]
If the system is larger than this, increase the sidemax parameter.
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Building initial approximation ...
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Adjusting initial point to fit the constraints
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Molecules of type: 1
Packing:|0 100%|
|*************************************************
Restraint-only function value: 3.9607206968837684E-004
Maximum violation of the restraints: 3.6155089782233198E-004
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Molecules of type: 2
Packing:|0 100%|
|***********************************
Restraint-only function value: 2.1866692126743645E-004
Maximum violation of the restraints: 2.1475355532781643E-004
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Rescaling maximum and minimum coordinates...
Computing size of patches...
Add fixed molecules to permanent arrays...
Reseting center of mass...
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Setting initial trial coordinates ...
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Molecules of type: 1
Adjusting random positions to fit the constraints.
Packing:|0 100%|
|
Restraint-only function value: 1.0075773399774217E-002
Maximum violation of the restraints: 3.6181280046880086E-003
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Molecules of type: 2
Adjusting random positions to fit the constraints.
Packing:|0 100%|
|
Restraint-only function value: 0.0000000000000000
Maximum violation of the restraints: 0.0000000000000000
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Objective function at initial point: 11991.278977083359
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Packing molecules of type: 1
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Starting GENCAN loop: 0
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|******************************************************************|
|*************************************************
Function value from last GENCAN loop: f = .25109E-01
Best function value before: f = .59578E+04
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: .99257E-02
Current structure written to file: system_init.pdb
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Packing solved for molecules of type 1
Objective function value: 2.5108756643450057E-002
Maximum violation of target distance: 0.0000000000000000
Max. constraint violation: 9.9256762733930040E-003
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################################################################################
Packing molecules of type: 2
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Starting GENCAN loop: 0
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|******************************************
Function value from last GENCAN loop: f = .43875E-05
Best function value before: f = .21528E+04
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: .43875E-05
Current structure written to file: system_init.pdb
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Packing solved for molecules of type 2
Objective function value: 4.3874553174474269E-006
Maximum violation of target distance: 0.0000000000000000
Max. constraint violation: 4.3874553174474269E-006
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################################################################################
Packing all molecules together
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Starting GENCAN loop: 0
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|******************************************************************|
|******************************************************************|
Function value from last GENCAN loop: f = .40398E+01
Best function value before: f = .39108E+04
Improvement from best function value: 99.90 %
Improvement from last loop: 99.90 %
Maximum violation of target distance: 0.369437
Maximum violation of the constraints: .72061E+00
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Starting GENCAN loop: 1
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|******************************************************************|
|******************************************************************|
Function value from last GENCAN loop: f = .20739E+00
Best function value before: f = .40398E+01
Improvement from best function value: 94.87 %
Improvement from last loop: 94.87 %
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .94398E-01
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Starting GENCAN loop: 2
Scaling radii by: 1.1000000000000001
Packing:|0 100%|
|*************************************************
Function value from last GENCAN loop: f = .36480E-01
Best function value before: f = .20739E+00
Improvement from best function value: 82.41 %
Improvement from last loop: 82.41 %
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .95830E-02
################################################################################
Success!
Final objective function value: .36480E-01
Maximum violation of target distance: 0.000000
Maximum violation of the constraints: .95830E-02
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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.
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Solution written to file: system_init.pdb
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Running time: 0.148391008 seconds.
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