Modules List

Here is a list of all modules with brief descriptions:

Malltimer	Module AllTimer Utility, independent of the rest of sda. Implemtent 2 methods : cpu time and clock time
Manalyze_subroutines	Module containing several subroutines that are used in other tools
Mcom_sda	Module with general small structures
Mgenbox_subroutines	Module declaration
Mmod_analytic	Analytical expressions, store energy and force in precomputed array
Mmod_array_protein	Module to define an array of proteins
Mmod_compute_analytic_2proteins
Mmod_compute_analytic_sdamm
Mmod_compute_crowder_sdamm
Mmod_compute_energy	Group all function to compute the energy for sda 2 proteins/ sda koff
Mmod_compute_energy_flex	Compute energy when changing conformation for sda_2proteins.
Mmod_compute_energy_sdamm	Module for computing energy, case sdamm
Mmod_compute_force	Module groups computation of forces and energies of sda_2proteins and related. simplify interface if all in one file
Mmod_compute_force_sdamm	Group all function for computing energy for sdamm.
Mmod_compute_image_charge	Group computation of force and energy when image charge is used. Some specific interactions are implemented for ProMetCS force field
Mmod_compute_metaldesolv	Used for metal desolvation computation
Mmod_compute_pmf
Mmod_crowder
Mmod_dqagi
Mmod_exclusion_grid	Define a specific type for exclusion grid
Mmod_flexibility	Module for flexibility
Mmod_force_energy	Only one single object of this module should be initialized
Mmod_geometry	Define a base class geometry and derivatives : sphere or box
Mmod_gouy_chapman
Mmod_grid	Module for dealing with 3 dimensional grids
Mmod_gridtype	Module grid and charges types Writen long time ago, convenient in force, but could evolve
Mmod_histogram	Module to define a histogram to store binned data
Mmod_hydrodynamics	Module Hydrodynamics. Only contain function, state independent
Mmod_info_printing
Mmod_init_position	Groups functions for intialisation of position. Include all random_position subroutines
Mmod_input_parameter	Contain all input parameter in an unique type Used only for reading and preparation, not anymore in the code after
Mmod_interface	Module for overloading function
Mmod_ljgrid	Module to define lennard-jones interaction
Mmod_onecomplexe	Module to define one_complexe Theses objects are stored in record
Mmod_parameters_ecm	Parameters for ECM
Mmod_pdb_type	Module to define a pdb type and pdb reading and writing routine for tools. prepare_atom_protein routine has poor modularity making use in tools difficult. – could be merged later – need to add into protein object structure
Mmod_protein	Module to define one protein (position, orientation, is surface?)
Mmod_rate_calculation	Define type association_rate
Mmod_rate_constant_calculation
Mmod_rate_constant_calculation_quadpack
Mmod_reactioncriteria	Module to define reaction criteria More informations on the reaction criteria page
Mmod_record	MODULE mod_record Define type record and subtypes Trajectory and ListComplexe
Mmod_residencetime	Residence time and rdf statistics
Mmod_sda_input
Mmod_set_parameters	Group functions to compute the cutoff, allocate dummy_array and energy array. used by all types of simulations
Mmod_setofgrid	Module for storing data needed for a specific conformation. store all grids and position of atoms
Mmod_type_calc	Define the type of calculation, and "false parralel" option
Mmod_van	Group VdW and test charges(for ECM) define predefined values which can be overwritten by the user (add_atoms file)
Mpar_zig_mod	For use with OpenMP
Msetup_sda	Module to simulate the setup of a sda run