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

Objects stored in the list ( for complexes ) or in the array ( for trajectory ) More...

Collaboration diagram for mod_onecomplexe::one_complexe:

Public Attributes

real(kind=8), dimension(:), allocatable real_ocompl
 energy terms, variable number but keep always the order : electrostatic, el desolvation, apolar desol (hydrophobic), repulsive lennard-jones, lennard-jones, image-charge More...
 
integer, dimension(:), allocatable int_ocompl
 intger to be stored: 1:ntraj, 2:nstep, 3:nprotein, 4: nconf More...
 
real(kind=8), dimension(:), allocatable other_real_ocompl
 Aditional terms: for trajectory time, for complexes occurence, average energy, deviation of energy terms
The standard deviation in only computed when the results are writen to disk, only the sum of the square is updated during the computation. More...
 
integer, dimension(:), allocatable box
 box info for sdamm, keep trace when a protein change box with PBC. Used only by tools for computing diffusion. More...
 
real(kind=8) sum_square_energy
 independent variable used during simulation, used for computing the standart deviation, temporary never printed or read More...
 
logical ibox
 if true, use the box information with PBC, could move into parent as well More...
 
real(kind=8), dimension(3) position
 coordinates and orientation, it has a fixed size and is mandatory More...
 
real(kind=8), dimension(3) orient_x
 
real(kind=8), dimension(3) orient_y
 

Detailed Description

Objects stored in the list ( for complexes ) or in the array ( for trajectory )

Allow variable number of fields :
integer terms ( trajectory number, step number, protein number and conformation) in int_compl
energy terms ( electrostatic, el. desolvation, apolar desol. (hydrophobic), repulsive lennard-jones ) in real_ocompl. They can be sum up ( el1-2 + el2-1 ) or writen separately
other real terms ( occurence, average total energy and standard deviation of the standard energy ) for complexes
or ( time ) for trajectory in other_real_ocompl

Print box informations when periodic boundary conditions are used
Can write the data in binary or ascii format

Member Data Documentation

◆ box

integer, dimension(:), allocatable mod_onecomplexe::one_complexe::box

box info for sdamm, keep trace when a protein change box with PBC. Used only by tools for computing diffusion.

◆ ibox

logical mod_onecomplexe::one_complexe::ibox

if true, use the box information with PBC, could move into parent as well

◆ int_ocompl

integer, dimension(:), allocatable mod_onecomplexe::one_complexe::int_ocompl

intger to be stored: 1:ntraj, 2:nstep, 3:nprotein, 4: nconf

◆ orient_x

real ( kind=8 ), dimension( 3 ) mod_onecomplexe::one_complexe::orient_x

◆ orient_y

real ( kind=8 ), dimension( 3 ) mod_onecomplexe::one_complexe::orient_y

◆ other_real_ocompl

real ( kind=8 ), dimension(:), allocatable mod_onecomplexe::one_complexe::other_real_ocompl

Aditional terms: for trajectory time, for complexes occurence, average energy, deviation of energy terms
The standard deviation in only computed when the results are writen to disk, only the sum of the square is updated during the computation.

◆ position

real ( kind=8 ), dimension( 3 ) mod_onecomplexe::one_complexe::position

coordinates and orientation, it has a fixed size and is mandatory

◆ real_ocompl

real ( kind=8 ), dimension(:), allocatable mod_onecomplexe::one_complexe::real_ocompl

energy terms, variable number but keep always the order : electrostatic, el desolvation, apolar desol (hydrophobic), repulsive lennard-jones, lennard-jones, image-charge

◆ sum_square_energy

real ( kind=8 ) mod_onecomplexe::one_complexe::sum_square_energy

independent variable used during simulation, used for computing the standart deviation, temporary never printed or read


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