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259 lines
10 KiB
259 lines
10 KiB
2 years ago
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################################################################################
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PACKMOL - Packing optimization for the automated generation of
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starting configurations for molecular dynamics simulations.
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Version 18.169
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################################################################################
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Packmol must be run with: packmol < inputfile.inp
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Userguide at: www.ime.unicamp.br/~martinez/packmol
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Reading input file... (Control-C aborts)
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Seed for random number generator: 1234567
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Output file: system_init.pdb
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Reading coordinate file: ../water/water_gaff.pdb
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Reading coordinate file: ../urea/URA_gaff.pdb
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Number of independent structures: 2
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The structures are:
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Structure 1 :../water/water_gaff.pdb( 3 atoms)
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Structure 2 :../urea/URA_gaff.pdb( 8 atoms)
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Maximum number of GENCAN loops for all molecule packing: 400
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Total number of restrictions: 2
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Distance tolerance: 2.5000000000000000
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Residue numbering set for structure 1 : 3
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Swap chains of molecules of structure 1 : F
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Residue numbering set for structure 2 : 3
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Swap chains of molecules of structure 2 : F
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Number of molecules of type 1 : 100
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Number of molecules of type 2 : 13
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Total number of atoms: 404
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Total number of molecules: 113
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Number of fixed molecules: 0
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Number of free molecules: 113
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Number of variables: 678
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Total number of fixed atoms: 0
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Maximum internal distance of type 1 : 1.5444600998407179
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Maximum internal distance of type 2 : 4.0422680514780316
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All atoms must be within these coordinates:
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x: [ -1000.0000000000000 , 1000.0000000000000 ]
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y: [ -1000.0000000000000 , 1000.0000000000000 ]
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z: [ -1000.0000000000000 , 1000.0000000000000 ]
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If the system is larger than this, increase the sidemax parameter.
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################################################################################
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Building initial approximation ...
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################################################################################
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Adjusting initial point to fit the constraints
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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Molecules of type: 1
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Packing:|0 100%|
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|*************************************************
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Restraint-only function value: 3.9607206968837684E-004
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Maximum violation of the restraints: 3.6155089782233198E-004
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--------------------------------------------------------------------------------
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Molecules of type: 2
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Packing:|0 100%|
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|***********************************
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Restraint-only function value: 2.1866692126743645E-004
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Maximum violation of the restraints: 2.1475355532781643E-004
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--------------------------------------------------------------------------------
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Rescaling maximum and minimum coordinates...
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Computing size of patches...
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Add fixed molecules to permanent arrays...
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Reseting center of mass...
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--------------------------------------------------------------------------------
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Setting initial trial coordinates ...
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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Molecules of type: 1
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Adjusting random positions to fit the constraints.
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Packing:|0 100%|
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Restraint-only function value: 1.0075773399774217E-002
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Maximum violation of the restraints: 3.6181280046880086E-003
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--------------------------------------------------------------------------------
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Molecules of type: 2
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Adjusting random positions to fit the constraints.
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Packing:|0 100%|
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Restraint-only function value: 0.0000000000000000
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Maximum violation of the restraints: 0.0000000000000000
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################################################################################
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Objective function at initial point: 11991.278977083359
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################################################################################
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Packing molecules of type: 1
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################################################################################
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--------------------------------------------------------------------------------
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Starting GENCAN loop: 0
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Scaling radii by: 1.1000000000000001
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Packing:|0 100%|
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|******************************************************************|
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|*************************************************
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Function value from last GENCAN loop: f = .25109E-01
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Best function value before: f = .59578E+04
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Improvement from best function value: 99.99 %
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Improvement from last loop: 99.99 %
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Maximum violation of target distance: 0.000000
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Maximum violation of the constraints: .99257E-02
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Current structure written to file: system_init.pdb
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--------------------------------------------------------------------------------
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Packing solved for molecules of type 1
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Objective function value: 2.5108756643450057E-002
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Maximum violation of target distance: 0.0000000000000000
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Max. constraint violation: 9.9256762733930040E-003
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--------------------------------------------------------------------------------
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################################################################################
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Packing molecules of type: 2
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################################################################################
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--------------------------------------------------------------------------------
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Starting GENCAN loop: 0
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Scaling radii by: 1.1000000000000001
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Packing:|0 100%|
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|******************************************
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Function value from last GENCAN loop: f = .43875E-05
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Best function value before: f = .21528E+04
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Improvement from best function value: 99.99 %
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Improvement from last loop: 99.99 %
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Maximum violation of target distance: 0.000000
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Maximum violation of the constraints: .43875E-05
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Current structure written to file: system_init.pdb
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--------------------------------------------------------------------------------
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Packing solved for molecules of type 2
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Objective function value: 4.3874553174474269E-006
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Maximum violation of target distance: 0.0000000000000000
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Max. constraint violation: 4.3874553174474269E-006
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--------------------------------------------------------------------------------
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################################################################################
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Packing all molecules together
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################################################################################
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--------------------------------------------------------------------------------
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Starting GENCAN loop: 0
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Scaling radii by: 1.1000000000000001
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Packing:|0 100%|
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|******************************************************************|
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|******************************************************************|
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Function value from last GENCAN loop: f = .40398E+01
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Best function value before: f = .39108E+04
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Improvement from best function value: 99.90 %
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Improvement from last loop: 99.90 %
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Maximum violation of target distance: 0.369437
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Maximum violation of the constraints: .72061E+00
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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Starting GENCAN loop: 1
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Scaling radii by: 1.1000000000000001
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Packing:|0 100%|
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|******************************************************************|
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|******************************************************************|
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Function value from last GENCAN loop: f = .20739E+00
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Best function value before: f = .40398E+01
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Improvement from best function value: 94.87 %
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Improvement from last loop: 94.87 %
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Maximum violation of target distance: 0.000000
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Maximum violation of the constraints: .94398E-01
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--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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Starting GENCAN loop: 2
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Scaling radii by: 1.1000000000000001
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Packing:|0 100%|
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|*************************************************
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Function value from last GENCAN loop: f = .36480E-01
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Best function value before: f = .20739E+00
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Improvement from best function value: 82.41 %
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Improvement from last loop: 82.41 %
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Maximum violation of target distance: 0.000000
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Maximum violation of the constraints: .95830E-02
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################################################################################
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Success!
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Final objective function value: .36480E-01
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Maximum violation of target distance: 0.000000
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Maximum violation of the constraints: .95830E-02
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--------------------------------------------------------------------------------
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Please cite this work if Packmol was useful:
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L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez,
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PACKMOL: A package for building initial configurations for
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molecular dynamics simulations.
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Journal of Computational Chemistry, 30:2157-2164,2009.
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################################################################################
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Solution written to file: system_init.pdb
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--------------------------------------------------------------------------------
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Running time: 0.148391008 seconds.
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--------------------------------------------------------------------------------
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