SDA (SDA flex)  7.2
Simulation of Diffusional Association
Public Attributes | List of all members
mod_protein::protein Type Reference

Define properties of one solute / protein. More...

Collaboration diagram for mod_protein::protein:

Public Attributes

integer, dimension(3) box
 keep trace of the box position, needed for sdamm More...
 
real(kind=8), dimension(3) position
 real position for sdamm, relative position for sda_2proteins More...
 
real(kind=8), dimension(3) center_protein
 center of geometry from the pdb file More...
 
integer id
 may be used by mod_record, keep it More...
 
real(kind=8) real_net_charge
 Local copy of real net charge (total charge) More...
 
type(sogrid), pointer p_sogrid
 pointer to the associated set of grid (sogrid) More...
 
type(flexible), pointer p_flex
 pointer to a flexible, only one of these two pointers should be initalized More...
 
logical local_copy
 If a local copy of the movable atoms is needed. More...
 
integer, dimension(:), pointer p_which_atom_surface
 one-dimensional array listing the atoms which are on the surface (order as in the orig.PDB file) More...
 
type(type_ljgrid), pointer p_pos_lenjones
 pointer to movable arrays for lennard-jones, contains all grids and position More...
 
real(kind=8), dimension(3) orientation_x
 For langevin integrator, not implementd. More...
 
real(kind=8), dimension(3) orientation_y
 
real(kind=8), dimension(3) orientation_z
 
real(kind=8) diff_trans
 local copy of diffusion coefficient. Maybe be modified by Hydrodynamic Interactions More...
 
real(kind=8) diff_rotat
 
logical surface
 General variable of the properties of the solute. More...
 
logical iflex
 
logical rotate
 
logical iimg_chg
 
logical vert_excl
 
integer nb_charge
 In case of local copy, size of the arrays. More...
 
integer nb_atom_surface
 
integer nb_rcriteria
 
logical imetaldesolv
 Parameter specific to metaldesolvation, grid owned by each protein. More...
 
real(kind=8), dimension(:,:), pointer array_mdesolv
 
integer size_metal
 
real(kind=8), dimension(:,:), pointer p_pos_charge
 pointers to the movable arrays if there is no local copy, they point to sogrid arrays
if there is a local copy needed, they allocate their own arrays
More...
 
real(kind=8), dimension(:,:), pointer p_list_atom_surface
 
real(kind=4), dimension(:,:), pointer p_pos_rcriteria
 

Detailed Description

Define properties of one solute / protein.

Contains :

Member Data Documentation

◆ array_mdesolv

real ( kind=8 ), dimension(:,:), pointer mod_protein::protein::array_mdesolv

◆ box

integer, dimension ( 3 ) mod_protein::protein::box

keep trace of the box position, needed for sdamm

◆ center_protein

real ( kind=8 ), dimension(3) mod_protein::protein::center_protein

center of geometry from the pdb file

◆ diff_rotat

real ( kind=8 ) mod_protein::protein::diff_rotat

◆ diff_trans

real ( kind=8 ) mod_protein::protein::diff_trans

local copy of diffusion coefficient. Maybe be modified by Hydrodynamic Interactions

◆ id

integer mod_protein::protein::id

may be used by mod_record, keep it

◆ iflex

logical mod_protein::protein::iflex

◆ iimg_chg

logical mod_protein::protein::iimg_chg

◆ imetaldesolv

logical mod_protein::protein::imetaldesolv

Parameter specific to metaldesolvation, grid owned by each protein.

◆ local_copy

logical mod_protein::protein::local_copy

If a local copy of the movable atoms is needed.

◆ nb_atom_surface

integer mod_protein::protein::nb_atom_surface

◆ nb_charge

integer mod_protein::protein::nb_charge

In case of local copy, size of the arrays.

◆ nb_rcriteria

integer mod_protein::protein::nb_rcriteria

◆ orientation_x

real ( kind=8 ), dimension(3) mod_protein::protein::orientation_x

For langevin integrator, not implementd.

orientation of the solute, store vector for the 3 axis

◆ orientation_y

real ( kind=8 ), dimension(3) mod_protein::protein::orientation_y

◆ orientation_z

real ( kind=8 ), dimension(3) mod_protein::protein::orientation_z

◆ p_flex

type ( flexible ), pointer mod_protein::protein::p_flex

pointer to a flexible, only one of these two pointers should be initalized

◆ p_list_atom_surface

real ( kind = 8 ), dimension(:,:), pointer mod_protein::protein::p_list_atom_surface

◆ p_pos_charge

real ( kind = 8 ), dimension(:,:), pointer mod_protein::protein::p_pos_charge

pointers to the movable arrays if there is no local copy, they point to sogrid arrays
if there is a local copy needed, they allocate their own arrays

◆ p_pos_lenjones

type ( type_ljgrid ), pointer mod_protein::protein::p_pos_lenjones

pointer to movable arrays for lennard-jones, contains all grids and position

◆ p_pos_rcriteria

real ( kind = 4 ), dimension(:,:), pointer mod_protein::protein::p_pos_rcriteria

◆ p_sogrid

type ( sogrid ), pointer mod_protein::protein::p_sogrid

pointer to the associated set of grid (sogrid)

◆ p_which_atom_surface

integer, dimension(:), pointer mod_protein::protein::p_which_atom_surface

one-dimensional array listing the atoms which are on the surface (order as in the orig.PDB file)

◆ position

real ( kind=8 ), dimension(3) mod_protein::protein::position

real position for sdamm, relative position for sda_2proteins

◆ real_net_charge

real ( kind=8 ) mod_protein::protein::real_net_charge

Local copy of real net charge (total charge)

◆ rotate

logical mod_protein::protein::rotate

◆ size_metal

integer mod_protein::protein::size_metal

◆ surface

logical mod_protein::protein::surface

General variable of the properties of the solute.

◆ vert_excl

logical mod_protein::protein::vert_excl

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