SDA  7.1
Simulation of Diffusional Association
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mod_compute_analytic_sdamm Module Reference
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Public Member Functions

subroutine force_analytic_dh_sdamm (tab_prot, geom, nb_prot, param_force_energy, all_force, all_torque)
 Compute force with analytic function. More...
 
subroutine pair_force_full_analytic_sdamm (prot1, prot2, pos_relat, type_p1, type_p2, dist, ff2, ff1)
 Compute full analytic expression
To see later if it can be common to sda and sdamm. not far. More...
 
subroutine pair_force_partial_analytic_sdamm (prot1, prot2, pos_relat, type_p1, type_p2, dist, ff2, ff1, tt2, tt1)
 Only partial analytic, loop over all atoms in this case.
Analytic DH is set to zero if inside the grid. More...
 
subroutine energy_analytic_dh_sdamm (tab_prot, geom, nb_prot, param_force_energy, array_energy)
 Compute energy for sdamm calculation.
. More...
 
subroutine pair_energy_full_analytic_sdamm (prot1, prot2, type_p1, type_p2, dist, energy1, energy2)
 Compute Full DH interactions.
. More...
 
subroutine pair_energy_partial_analytic_sdamm (prot1, prot2, pos_relat, type_p1, type_p2, dist, energy1, energy2)
 Only partial analytic, loop over all atoms in this case.
Analytic has been set to zero if inside the grid. More...
 

Member Function/Subroutine Documentation

subroutine mod_compute_analytic_sdamm::energy_analytic_dh_sdamm ( type ( array_protein_type ), intent(in), 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 ( :,: )  array_energy 
)

Compute energy for sdamm calculation.
.

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
array_energy: return updated array_energy

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subroutine mod_compute_analytic_sdamm::force_analytic_dh_sdamm ( type ( array_protein_type ), intent(in), 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 ( :,: )  all_force,
real ( kind=8 ), dimension ( :,: )  all_torque 
)

Compute force with analytic function.

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

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subroutine mod_compute_analytic_sdamm::pair_energy_full_analytic_sdamm ( type ( protein ), intent(in)  prot1,
type ( protein ), intent(in)  prot2,
integer  type_p1,
integer  type_p2,
real( kind=4 ), intent(in)  dist,
real ( kind=8 ), intent(out)  energy1,
real ( kind=8 ), intent(out)  energy2 
)

Compute Full DH interactions.
.

Compute p2 solute in DH "grid" of p1

Parameters
prot1,prot2: olute 1 and 2, instance of protein
type_p1,type_p2: integer to get the type of solute
dist: distance between the solutes
energy1,energy2: return the energy of solute 1 and 2

Directly in kT

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subroutine mod_compute_analytic_sdamm::pair_energy_partial_analytic_sdamm ( type ( protein ), intent(in)  prot1,
type ( protein ), intent(in)  prot2,
real ( kind=8 ), dimension(3), intent(in)  pos_relat,
integer  type_p1,
integer  type_p2,
real ( kind=4 )  dist,
real ( kind=8 ), intent(out)  energy1,
real ( kind=8 ), intent(out)  energy2 
)

Only partial analytic, loop over all atoms in this case.
Analytic has been set to zero if inside the grid.

Parameters
prot1,prot2: olute 1 and 2, instance of protein
pos_relat: relative position
type_p1,type_p2: integer to get the type of solute
dist: distance between the solutes
energy1,energy2: return the energy of solute 1 and 2

Directly in kT

Directly to kT

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subroutine mod_compute_analytic_sdamm::pair_force_full_analytic_sdamm ( type ( protein ), intent(in)  prot1,
type ( protein ), intent(in)  prot2,
real ( kind=8 ), dimension ( 3 ), intent(in)  pos_relat,
integer  type_p1,
integer  type_p2,
real( kind=4 ), intent(in)  dist,
real ( kind=8 ), dimension ( 3 ), intent(out)  ff2,
real ( kind=8 ), dimension ( 3 ), intent(out)  ff1 
)

Compute full analytic expression
To see later if it can be common to sda and sdamm. not far.

Parameters
prot1,prot2: instance of protein
pos_relat: position relative
type_p1,type_p2: integer for the solute type
dist: distance between the 2 solutes
ff2,ff1: return force on solute 2 and 1, should be exactly the same with full analytic

Convert to kT/A

Convert to kT/A

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subroutine mod_compute_analytic_sdamm::pair_force_partial_analytic_sdamm ( type ( protein ), intent(in)  prot1,
type ( protein ), intent(in)  prot2,
real ( kind=8 ), dimension(3), intent(in)  pos_relat,
integer  type_p1,
integer  type_p2,
real ( kind=4 )  dist,
real ( kind=8 ), dimension ( 3 ), intent(out)  ff2,
real ( kind=8 ), dimension ( 3 ), intent(out)  ff1,
real ( kind=8 ), dimension ( 3 ), intent(out)  tt2,
real ( kind=8 ), dimension ( 3 ), intent(out)  tt1 
)

Only partial analytic, loop over all atoms in this case.
Analytic DH is set to zero if inside the grid.

Parameters
prot1,prot2: solute 1 and 2, instance of protein
pos_relat: relative position
type_p1,type_p2: integer to get the type of solute
dist: distance between the solutes
ff2,ff1,tt2,tt1: return the torque and force for the 2 solutes

Convert to kT/A

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