######################################################## # # # SUPER HAPPY LUCKY UNITED ATOM CONFIGURATION FILE # # # ######################################################## # Directory where to write all the map files to output-directory = /home/robert/Results/UA # File or directory #pdb-target = /home/robert/PDBs #pdb-target = pdbs #pdb-target = pdbs/crystal/1n5u.pdb pdb-target = /home/robert/PDBs/model_01.pdb # Radii to test. This can be a single number, or a list of comma seperated numbers enclosed by [] #nanoparticle-radius = [ 2.5, 5, 10, 20, 40, 50, 80, 100 ] nanoparticle-radius = 45 # Directory where the pfm files are located #pmf-directory = surface/Au/FCC/100/sca #pmf-directory = surface/CdSe/Wurtzite/2-10/sca pmf-directory = surface/SiO2-Amorphous # Hamaker file containing the hamaker constants. Must be in the format from David's notebook script (ask David) #hamaker-file = hamaker/Au.dat #hamaker-file = hamaker/tio2.dat #hamaker-file = hamaker/CdSe.dat hamaker-file = hamaker/SiO2_Amorph.dat # Enable the relevent potential. Comment out a potential to remove it from the simulation enable-surface enable-core enable-electrostatic # Simulation parameters. simulation-steps = 2000 #potential-cutoff = 5.0 potential-cutoff = 10.0 potential-size = 1000 angle-delta = 5.0 # Electrostatic potential control parameters. All lenghts are in nm and the zeta potential is in Volts bjerum-length = 0.8 debye-length = 0.7 #zeta-potential = [ -0.02, 0.0, 0.02 ] zeta-potential = [ 0.027 ] # A list of the molecules involved in the simulation. Even though they are called amino-acids, they can be any biomolecule amino-acids = [ ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL ] # charge for each biomolecule amino-acid-charges = [ 0.0, 1.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.5, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 ] ######################################################## # Radii of the molecules in the amino-acids list in nm # ######################################################## # vdW radius #amino-acid-radii = [ 0.50, 0.66, 0.57, 0.56, 0.55, 0.60, 0.59, 0.45, 0.45, 0.62, 0.62, 0.64, 0.64, 0.64, 0.56, 0.52, 0.56, 0.68, 0.65, 0.59 ] # spec-volume radius #amino-acid-radii = [ 0.267, 0.346, 0.299, 0.294, 0.289, 0.319, 0.318, 0.236, 0.244, 0.334, 0.334, 0.335, 0.334, 0.351, 0.300, 0.271, 0.298, 0.374, 0.353, 0.314 ] # radius of gyration #amino-acid-radii = [ 0.077437, 0.228465, 0.135142, 0.172925, 0.164715, 0.143993, 0.186783, 0.106399, 0.182331, 0.131446, 0.110508, 0.225361, 0.100557, 0.211873, 0.102759, 0.148555, 0.142513, 0.225805, 0.259114, 0.129323 ] # Average of vdW and spec-volume #amino-acid-radii = [ 0.320875, 0.416806, 0.360160, 0.354100, 0.348040, 0.383588, 0.381691, 0.284281, 0.292630, 0.400923, 0.400923, 0.403633, 0.402578, 0.420287, 0.360380, 0.326699, 0.358294, 0.44764, 0.42326, 0.377526 ] amino-acid-radii = [ 0.322715, 0.428767, 0.361551, 0.35600, 0.352205, 0.385727, 0.376055, 0.284623, 0.301896, 0.400987, 0.400987, 0.404922, 0.401799, 0.420854, 0.362305, 0.327697, 0.357403, 0.448826, 0.424851, 0.377343 ]