################################################################################ PACKMOL - Packing optimization for the automated generation of starting configurations for molecular dynamics simulations. Version 18.169 ################################################################################ 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. ################################################################################ Building initial approximation ... ################################################################################ Adjusting initial point to fit the constraints -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Packing:|0 100%| |************************************************* Restraint-only function value: 3.9607206968837684E-004 Maximum violation of the restraints: 3.6155089782233198E-004 -------------------------------------------------------------------------------- Molecules of type: 2 Packing:|0 100%| |*********************************** Restraint-only function value: 2.1866692126743645E-004 Maximum violation of the restraints: 2.1475355532781643E-004 -------------------------------------------------------------------------------- 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: 1.0075773399774217E-002 Maximum violation of the restraints: 3.6181280046880086E-003 -------------------------------------------------------------------------------- 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 ################################################################################ Objective function at initial point: 11991.278977083359 ################################################################################ Packing molecules of type: 1 ################################################################################ -------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------- ################################################################################ Packing molecules of type: 2 ################################################################################ -------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------- ################################################################################ Packing all molecules together ################################################################################ -------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------- 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. ################################################################################ Solution written to file: system_init.pdb -------------------------------------------------------------------------------- Running time: 0.148391008 seconds. --------------------------------------------------------------------------------