SDA (SDA flex)  7.2
Simulation of Diffusional Association
Functions/Subroutines
mod_compute_force_sdamm Module Reference

Group all function for computing energy for sdamm.
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Functions/Subroutines

subroutine force_epedhdlj_sdamm (tab_prot, geom, nb_prot, param_force_energy, all_force, all_torque, dummy_array)
 Compute forces and torques for sdamm, simple version, easier to extend. More...
 
subroutine compute_force_sdamm_2proteins (prot1, prot2, pos_relat, grid_number, dummy_array, ff1, ff2, tt1, tt2, subgrid, type_p1, type_p2, test_dist2)
 Compute forces and torques for one pair of solutes and one interaction.
. More...
 
subroutine force_epedhdlj_sdamm_fast (tab_prot, geom, nb_prot, param_force_energy, all_force, all_torque, dummy_array)
 Compute forces for sdamm with the fast algorithm. More...
 
subroutine compute_force_sdamm_2proteins_fast (prot1, prot2, pos_relat, grid_number, dummy_array, ff1_n, ff2_n, tt1_n, tt2_n, type_p1, type_p2, test_dist2)
 Compute forces and torques for one pair of solutes and one interaction. More...
 
subroutine compute_force_couple_sdamm_fast (prot1, prot2, pos_relat, nb_grid1, nb_grid2, gridtype, dummy_array, ff1_n, ff2_n, tt1_n, tt2_n, type_p1, type_p2, test_dist2)
 Compute forces and torques of two interactions, for one pair of solutes. More...
 

Detailed Description

Group all function for computing energy for sdamm.
.

Function/Subroutine Documentation

◆ compute_force_couple_sdamm_fast()

subroutine mod_compute_force_sdamm::compute_force_couple_sdamm_fast ( type ( protein ), intent(in)  prot1,
type ( protein ), intent(in)  prot2,
real ( kind=8 ), dimension( 3 ), intent(inout)  pos_relat,
integer, intent(in)  nb_grid1,
integer, intent(in)  nb_grid2,
integer, intent(in)  gridtype,
real ( kind=8 ), dimension ( : ), intent(in), target  dummy_array,
real ( kind=8 ), dimension( 3 ), intent(inout)  ff1_n,
real ( kind=8 ), dimension( 3 ), intent(inout)  ff2_n,
real ( kind=8 ), dimension( 3 ), intent(inout)  tt1_n,
real ( kind=8 ), dimension( 3 ), intent(inout)  tt2_n,
integer, intent(in)  type_p1,
integer, intent(in)  type_p2,
real (kind=4), intent(in)  test_dist2 
)

Compute forces and torques of two interactions, for one pair of solutes.

Compute a couple of interactions in the same loop, do not check for asymetries Fastest method

Parameters
prot1,prot2: instance of protein
pos_relat: relative position between the 2 solutes
nb_grid1,nb_grid2: number of the grids, refer to mod_gridtype
gridtype: 1 or 2 used to know which couple of interactions to compute
dummy_array: used for repulsive lennard-jones interactions
ff1_n,ff2_n,tt1_n,tt2_n: return forces and torques on solutes 1 and 2
type_p1,type_p2: integer type of the solutes
test_dist2: distance square between the solutes
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◆ compute_force_sdamm_2proteins()

subroutine mod_compute_force_sdamm::compute_force_sdamm_2proteins ( type ( protein ), intent(in)  prot1,
type ( protein ), intent(in)  prot2,
real ( kind=8 ), dimension ( 3 ), intent(in)  pos_relat,
integer, intent(in)  grid_number,
real ( kind=8 ), dimension ( : ), intent(in), target  dummy_array,
real ( kind=8 ), dimension( 3 ), intent(out)  ff1,
real ( kind=8 ), dimension( 3 ), intent(out)  ff2,
real ( kind=8 ), dimension( 3 ), intent(out)  tt1,
real ( kind=8 ), dimension( 3 ), intent(out)  tt2,
integer, intent(in)  subgrid,
integer, intent(in)  type_p1,
integer, intent(in)  type_p2,
real (kind=4), intent(in)  test_dist2 
)

Compute forces and torques for one pair of solutes and one interaction.
.

Explicitely check if there iare asymetries

Parameters
prot1,prot2: instance of protein
pos_relat: relative position between the 2 solutes
grid_number: number of the grid, refer to mod_gridtype
dummy_array: used for repulsive lennard-jones interactions
ff1,ff2,tt1,tt2: return forces and torques on solutes 1 and 2
subgrid: sub-grid number, normally one (used for LJ)
type_p1,type_p2: Solute types for interacting solutes
type_p1,type_p2: integer type of the solutes
test_dist2: distance square between the solutes
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◆ compute_force_sdamm_2proteins_fast()

subroutine mod_compute_force_sdamm::compute_force_sdamm_2proteins_fast ( type ( protein ), intent(in)  prot1,
type ( protein ), intent(in)  prot2,
real ( kind=8 ), dimension (3 )  pos_relat,
integer, intent(in)  grid_number,
real ( kind=8 ), dimension ( : ), intent(in)  dummy_array,
real ( kind=8 ), dimension( 3 ), intent(inout)  ff1_n,
real ( kind=8 ), dimension( 3 ), intent(inout)  ff2_n,
real ( kind=8 ), dimension( 3 ), intent(inout)  tt1_n,
real ( kind=8 ), dimension( 3 ), intent(inout)  tt2_n,
integer, intent(in)  type_p1,
integer, intent(in)  type_p2,
real (kind=4), intent(in)  test_dist2 
)

Compute forces and torques for one pair of solutes and one interaction.

Do nopt check for asymetries in this case.

Parameters
prot1,prot2: instance of protein
pos_relat: relative position between the 2 solutes
grid_number: number of the grid, refer to mod_gridtype
dummy_array: used for repulsive lennard-jones interactions
ff1_n,ff2_n,tt1_n,tt2_n: return forces and torques on solutes 1 and 2
type_p1,type_p2: Solute types for interacting solutes
type_p1,type_p2: integer type of the solutes
test_dist2: distance square between the solutes
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◆ force_epedhdlj_sdamm()

subroutine mod_compute_force_sdamm::force_epedhdlj_sdamm ( type ( array_protein_type ), target  tab_prot,
type ( geometry ), intent(in)  geom,
integer, intent(in)  nb_prot,
type ( type_force_energy ), intent(in)  param_force_energy,
real ( kind=8 ), dimension ( : , : ), intent(out)  all_force,
real ( kind=8 ), dimension ( : , : ), intent(out)  all_torque,
real ( kind=8 ), dimension( : ), target  dummy_array 
)

Compute forces and torques for sdamm, simple version, easier to extend.

Parameters
tab_prot: instance of array_protein_type
geom: instance of geometry
nb_prot: total number of solutes
param_force_energy: instance of type_force_energy
all_force,all_torque: return all forces and torques
dummy_array: used for repulsive lennard-jones interactions
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◆ force_epedhdlj_sdamm_fast()

subroutine mod_compute_force_sdamm::force_epedhdlj_sdamm_fast ( type ( array_protein_type ), target  tab_prot,
type ( geometry ), intent(in)  geom,
integer  nb_prot,
type ( type_force_energy ), intent(in)  param_force_energy,
real ( kind=8 ), dimension ( : , : ), intent(out)  all_force,
real ( kind=8 ), dimension ( : , : ), intent(out)  all_torque,
real ( kind=8 ), dimension ( : ), intent(in)  dummy_array 
)

Compute forces for sdamm with the fast algorithm.

If possible compute a couple of interactions at the same type

Parameters
tab_prot: instance of array_protein_type
geom: instance of geometry
nb_prot: total number of solutes
param_force_energy: instance of type_force_energy
dummy_array: used for repulsive lennard-jones interactions
all_force,all_torque: return all forces and torques
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