SDA  7.1
Simulation of Diffusional Association
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File List
Here is a list of all documented files with brief descriptions:
o*alltimer.f90Module to define the timers for time performance
o*bd_move.f90Implement functions for BD translation and rotation, boost
o*change_conformation.f90Functions used for the change of conformation
o*check_exclusion.f90Check if protein 2 overlaps with protein 1
o*check_reaction_pair.f90Check if the reaction pairs are satisfied between protein 1 and 2.
Include all cases : docking, association rate and electron transfert
o*compute_distance.f90General functions to compute the distance between 2 proteins
o*eschk.f90Check escape of solute 2.
o*init_time.f90Define the timestep ( variable for sda_2proteins )
o*main.f90Main program
o*MainLoop_sda_2proteins.f90Version of test, without OpenMP parralellisation
o*MainLoop_sda_2proteins_omp.f90Parralel version of sda 2proteins with OpenMP
o*MainLoop_sda_energy.f90Loop for sda_energy
o*MainLoop_sda_pmf.f90Loop for sda_pmf
o*MainLoop_sdamm.f90Loop in the case of multiple proteins
o*make_bd_move_2prot.f90Apply the BD translation and rotation to the solutes
o*make_bd_move_2prot_timer_excl.f90Same as make_bd_move_2prot, but use timer_excl as input ( could be optional )
o*make_bd_move_sdamm.f90Make the BD motion in the case of a sdamm simulation
o*make_exclusion_grid.f90Compute the exclusion grid, only for sda_2proteins and solute 1
o*maths.fGroup general mathematical functions
o*maths_thread_safe.f90Implement thread-safe mathematical subroutines which deals with RGN
o*mod_analytic.f90Define analytical interactions, stored in 1D array
o*mod_array_protein.f90Define an array where all proteins are stored
o*mod_compute_analytic_2proteins.f90Compute force and energies for analytic interaction (DH for now) for sda_2proteins
o*mod_compute_analytic_sdamm.f90Analytic (DH/crowder) Force and energy computation for SDAMM.
o*mod_compute_energy.f90Group energy computation for sda_2proteins
o*mod_compute_energy_flex.f90Used for evaluating energy when there is a change of conformation
o*mod_compute_energy_sdamm.f90Group energy functions for sdamm
o*mod_compute_force.f90Group functions to compute force for 2 proteins
o*mod_compute_force_sdamm.f90All functions to compute force in sdamm (OpenMP loop)
o*mod_compute_image_charge.f90Compute image charge for metal surface (2 proteins and sdamm)
o*mod_compute_metaldesolv.f90Compute metal desolvation (ProMetCS) for 2 proteins and sdamm
o*mod_compute_pmf.f90Group functions for the computation of PMF on
o*mod_exclusion_grid.f90Define the exclusion grid
o*mod_flexibility.f90Allow the change in conformation of the solutes
o*mod_force_energy.f90Regroup information useful for computing force and energy with version fast
o*mod_geometry.f90Define geometric properties of the simulation box
o*mod_grid.f90Define 3D UHBD
o*mod_gridtype.f90Enumeration and function of the different grids and charges and array used in sda
o*mod_hydrodynamics.f90Function for volume fraction and rescaling of parameters HI on trans. diff and rot. diff (Tokuyama for tr. diff. and Cichocki for rot. diff.)
o*mod_init_position.f90Group functions for setting the initial position
o*mod_input_parameter.f90List all parameters in use for sda and some of the tools
o*mod_interface.f90Define the equivalent of overloading functions. Only read_value() at this point
o*mod_ljgrid.f90Declare lennard-jones grid (only for ProMetCS force field)
o*mod_onecomplexe.f90Define a single "line" for complexes or trajectory file
o*mod_par_zig.f90Thread-safe random generator with the ziggurat method
o*mod_protein.f90Define one protein or solute
o*mod_rate_calculation.f90Module for rates calculation, electron transfer and first passage time
o*mod_ReactionCriteria.f90Define reaction criteria
o*mod_record.f90Module for reading and writing trajectories and complexes files
o*mod_ResidenceTime.f90Compute, store and print all residence time and the radial distribution function with sdamm
o*mod_sda_new_common.f90Define general types and global variables
o*mod_set_parameters.f90Group the setting of cutoff, rhit ( distance for overlap testing), array of energies and dummy_array (used by all simulations)
o*mod_setofgrid.f90Store all grids and position of atoms
o*mod_type_calculation.f90Define the type of the calculation : sda_2proteins, sda_energy, sdamm,..
o*mod_van.f90For Van der Walls and test carges setup
o*prepare_atom_protein.f90Call by prepare_grid.f90 for setting atom position and exclusion grid
o*prepare_grid.f90Load the grids and call prepare_atom_protein
o*read_eff_charges.f90Read the effective charges
o*read_group_file.f90Read all parameters of one specific GROUP from the sda input file
o*read_input_file.f90Main function to read sda input file
o*read_pdb.f90Subroutine read_pdb()
o*restart.f90To read and write restart file
o*solva.f90Define an approximate calculation of the solvant accessibility
o*solva_naccess.f90Compute solvent accessibility with naccess algorithm
\*utils.f90Utilities functions