SDA  7.1
Simulation of Diffusional Association
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mod_setofgrid::sogrid Type Reference

Store all grids ( UHBD type), and "charges": charges, accessibility and their position. More...

Collaboration diagram for mod_setofgrid::sogrid:

Public Attributes

real(kind=8), dimension(:,:),
allocatable 
position_charge
 position of the effective charge
 
real(kind=4), dimension(:,:),
allocatable 
reaction_criteria_pos
 reaction criteria associated to this set of grid make sense for sda flex, for sdamm ?? by default associated to protein2 change associate to all proteins we want to consider possible criteria seems easier to store only array of position for sda_flex and sdamm, limitation if HOMODIMER !!
 
type(type_grid), dimension(:),
pointer 
pset_grid
 fixed size array which contains pointers to grid objects ( uhbd type): electrostatic, desolvation, hydrophobic, lennard-jones repulsive ( sdamm ), lennar-jones
 
type(analytic), dimension(:),
pointer 
pset_analytic_grid
 fixed size array which contains pointers to analytical grid
 
type(type_grid_excl), pointer p_excl_grid
 pointer to exclusion grid
 
type(type_ljgrid), pointer p_ljgrid
 pointer to module mod_ljgrid, include all grids, all atoms
 
real(kind=8) charge_total
 
integer nb_charge
 
integer nb_atom_surface
 
integer nb_reaction_criteria
 
real(kind=8) diffusion_trans
 rotation and translation diffusion coefficients, as read in the input file

 
real(kind=8) diffusion_rotat
 
real(kind=8) stoke_radius
 In case of hydrodynamic interaction stoke_radius must be > 0. Used by Debye-Huckel also now, need to correct / test for HI, explict hi variable needed.
 
logical idebye
 Save if debye-huckel / analytical interaction is activated Needed because full load done only later by param_force_energy.
 
real(kind=4), dimension(:,:),
allocatable 
cut2_array
 Array to store cut off for each grid in sogrid with equivalent in all other sogrids.
 
real(kind=4) max_cut2
 Largest cut off in cut2_array.
 
real(kind=8), dimension(:),
allocatable 
charge_grid
 value of the effective charge, and square value for desolvation
 
real(kind=8), dimension(:),
allocatable 
charge_square_grid
 
real(kind=8), dimension(:,:),
allocatable 
list_atom_surface
 accessibility position of the atoms at the surface, computed by solva()
 
real(kind=8), dimension(:),
allocatable 
accessibility
 
integer, dimension(:), allocatable which_atom_surface
 array listing which atoms from the entire PDB list are the surface atoms (i.e., accessible) - used only in tools
 
logical alloc_which_at_surf
 should this array be allocated? default: false
 
real(kind=8) hexcl
 parameter for exclusion, put it here even if not implemented
keep old format because old subroutine
 
real(kind=8) distance_max
 

Detailed Description

Store all grids ( UHBD type), and "charges": charges, accessibility and their position.

Pointer to exclusion grid as well, see mod_exclusion_grid.f90
Many proteins may refer to the same instance of sogrid ( case of sdamm )


The documentation for this type was generated from the following file: