![]() ![]() | Module to define the timers for time performance |
![]() ![]() | Implement functions for BD translation and rotation, boost |
![]() ![]() | Functions used for the change of conformation |
![]() ![]() | Check if protein 2 overlaps with protein 1 |
![]() ![]() | Check if the reaction pairs are satisfied between protein 1 and 2. Include all cases : docking, association rate and electron transfert |
![]() ![]() | General functions to compute the distance between 2 proteins |
![]() ![]() | Check escape of solute 2. |
![]() ![]() | Define the timestep ( variable for sda_2proteins ) |
![]() ![]() | Main program |
![]() ![]() | Version of test, without OpenMP parralellisation |
![]() ![]() | Parralel version of sda 2proteins with OpenMP |
![]() ![]() | Loop for sda_energy |
![]() ![]() | Loop for sda_pmf |
![]() ![]() | Loop in the case of multiple proteins |
![]() ![]() | Apply the BD translation and rotation to the solutes |
![]() ![]() | Same as make_bd_move_2prot, but use timer_excl as input ( could be optional ) |
![]() ![]() | Make the BD motion in the case of a sdamm simulation |
![]() ![]() | Compute the exclusion grid, only for sda_2proteins and solute 1 |
![]() ![]() | Group general mathematical functions |
![]() ![]() | Implement thread-safe mathematical subroutines which deals with RGN |
![]() ![]() | Define analytical interactions, stored in 1D array |
![]() ![]() | Define an array where all proteins are stored |
![]() ![]() | Compute force and energies for analytic interaction (DH for now) for sda_2proteins |
![]() ![]() | Analytic (DH/crowder) Force and energy computation for SDAMM. |
![]() ![]() | Group energy computation for sda_2proteins |
![]() ![]() | Used for evaluating energy when there is a change of conformation |
![]() ![]() | Group energy functions for sdamm |
![]() ![]() | Group functions to compute force for 2 proteins |
![]() ![]() | All functions to compute force in sdamm (OpenMP loop) |
![]() ![]() | Compute image charge for metal surface (2 proteins and sdamm) |
![]() ![]() | Compute metal desolvation (ProMetCS) for 2 proteins and sdamm |
![]() ![]() | Group functions for the computation of PMF on |
![]() ![]() | Define the exclusion grid |
![]() ![]() | Allow the change in conformation of the solutes |
![]() ![]() | Regroup information useful for computing force and energy with version fast |
![]() ![]() | Define geometric properties of the simulation box |
![]() ![]() | Define 3D UHBD |
![]() ![]() | Enumeration and function of the different grids and charges and array used in sda |
![]() ![]() | Function for volume fraction and rescaling of parameters HI on trans. diff and rot. diff (Tokuyama for tr. diff. and Cichocki for rot. diff.) |
![]() ![]() | Group functions for setting the initial position |
![]() ![]() | List all parameters in use for sda and some of the tools |
![]() ![]() | Define the equivalent of overloading functions. Only read_value() at this point |
![]() ![]() | Declare lennard-jones grid (only for ProMetCS force field) |
![]() ![]() | Define a single "line" for complexes or trajectory file |
![]() ![]() | Thread-safe random generator with the ziggurat method |
![]() ![]() | Define one protein or solute |
![]() ![]() | Module for rates calculation, electron transfer and first passage time |
![]() ![]() | Define reaction criteria |
![]() ![]() | Module for reading and writing trajectories and complexes files |
![]() ![]() | Compute, store and print all residence time and the radial distribution function with sdamm |
![]() ![]() | Define general types and global variables |
![]() ![]() | Group the setting of cutoff, rhit ( distance for overlap testing), array of energies and dummy_array (used by all simulations) |
![]() ![]() | Store all grids and position of atoms |
![]() ![]() | Define the type of the calculation : sda_2proteins, sda_energy, sdamm,.. |
![]() ![]() | For Van der Walls and test carges setup |
![]() ![]() | Call by prepare_grid.f90 for setting atom position and exclusion grid |
![]() ![]() | Load the grids and call prepare_atom_protein |
![]() ![]() | Read the effective charges |
![]() ![]() | Read all parameters of one specific GROUP from the sda input file |
![]() ![]() | Main function to read sda input file |
![]() ![]() | Subroutine read_pdb() |
![]() ![]() | To read and write restart file |
![]() ![]() | Define an approximate calculation of the solvant accessibility |
![]() ![]() | Compute solvent accessibility with naccess algorithm |
![]() ![]() | Utilities functions |