mod_compute_analytic_2proteins Module Reference

Functions/Subroutines
subroutine	force_analytic_dh (tab_protein, param_force_energy, dist, f, t, t1)
	Compute force with analytic function. Values precomputed and stored in an array Seems necessary to make separate for dh ? easier.
subroutine	pair_force_full_analytic_2proteins (prot1, prot2, type_p1, type_p2, dist, ff2, ff1)
	Compute force if solute and grids do not overlap p2 solute in DH "grid" of p1, and opposite. .
subroutine	pair_force_partial_analytic_2proteins (prot1, prot2, type_p1, type_p2, dist, ff2, ff1, tt2, tt1)
	Only partial analytic, loop over all atoms in this case Analytic is set to zero if inside the cutoff.
subroutine	energy_analytic_dh (tab_protein, param_force_energy, dist, array_energy)
	Compute energy with analytic function Seems necessary to make separate for dh ? easier.. to see later.
subroutine	pair_energy_full_analytic_2proteins (prot1, prot2, type_p1, type_p2, dist, energy1, energy2)
	Compute Full DH interactions. Need to split, cutoffs may be different/ asymetric between p1 and p2. Only compute El-DH prot1 in analytical grid of protein 2 ( all grids stored in prot2 % p_sogrid % pset_analytical) Not good for 2 proteins because asymetry between static/mobil solute Need to test cutoffs for each interaction.
subroutine	pair_energy_partial_analytic (prot1, prot2, 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 Asymetry due to cutoffs.
subroutine	force_analytic_dh_imgchg (tab_protein, param_force_energy, dist, f, t)
	Compute forces for image charge DH routine NJB: Changed to move reflection plane to edge atomic layer when surface more than one atom.
subroutine	force_full_analytic_dh_imgchg (prot2, type_p2, dist, mirror_z, ff_analytic)
subroutine	force_partial_analytic_dh_imgchg (prot2, type_p2, dist, mirror_z, ff_partial, tt_partial)
subroutine	energy_analytic_dh_imgchg (tab_protein, param_force_energy, dist, array_energy)
subroutine	energy_full_analytic_dh_imgchg (prot2, type_p2, dist, mirror_z, energy2_analytic)
subroutine	energy_partial_analytic_dh_imgchg (prot2, type_p2, dist, mirror_z, energy2_partial)
subroutine	force_analytic_hom_charged_surf (tab_protein, param_force_energy, dist, f, t)
subroutine	force_full_analytic_hom_charged_surf (prot1, prot2, type_p2, dist, ff_analytic)
subroutine	force_partial_analytic_hom_charged_surf (prot1, prot2, type_p2, dist, ff_partial, tt_partial)
subroutine	energy_analytic_hom_charged_surf (tab_protein, param_force_energy, dist, array_energy)
subroutine	energy_full_analytic_hom_charged_surf (prot1, prot2, type_p2, dist, energy2_analytic)
subroutine	energy_partial_analytic_hom_charged_surf (prot1, prot2, type_p2, dist, energy2_partial)

Function/Subroutine Documentation

energy_analytic_dh()

subroutine mod_compute_analytic_2proteins::energy_analytic_dh	(	type ( array_protein_type ), intent(in), target	tab_protein,
		type ( type_force_energy ), intent(in)	param_force_energy,
		real( kind=4 ), intent(in)	dist,
		real ( kind=8 ), dimension (:,:), intent(inout)	array_energy
	)

Compute energy with analytic function Seems necessary to make separate for dh ? easier.. to see later.

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energy_analytic_dh_imgchg()

subroutine mod_compute_analytic_2proteins::energy_analytic_dh_imgchg	(	type ( array_protein_type ), intent(in), target	tab_protein,
		type ( type_force_energy ), intent(in)	param_force_energy,
		real( kind=4 ), intent(in)	dist,
		real ( kind=8 ), dimension (:,:), intent(inout)	array_energy
	)

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energy_analytic_hom_charged_surf()

subroutine mod_compute_analytic_2proteins::energy_analytic_hom_charged_surf	(	type(array_protein_type), intent(in), target	tab_protein,
		type(type_force_energy), intent(in)	param_force_energy,
		real(kind=4), intent(in)	dist,
		real(kind=8), dimension(:,:), intent(inout)	array_energy
	)

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energy_full_analytic_dh_imgchg()

subroutine mod_compute_analytic_2proteins::energy_full_analytic_dh_imgchg	(	type ( protein ), intent(in)	prot2,
		integer	type_p2,
		real( kind=4 ), intent(in)	dist,
		real( kind=8 ), intent(in)	mirror_z,
		real ( kind=8 ), intent(out)	energy2_analytic
	)

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energy_full_analytic_hom_charged_surf()

subroutine mod_compute_analytic_2proteins::energy_full_analytic_hom_charged_surf	(	type(protein), intent(in)	prot1,
		type(protein), intent(in)	prot2,
		integer	type_p2,
		real(kind=4), intent(in)	dist,
		real(kind=8), intent(out)	energy2_analytic
	)

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energy_partial_analytic_dh_imgchg()

subroutine mod_compute_analytic_2proteins::energy_partial_analytic_dh_imgchg	(	type ( protein ), intent(in)	prot2,
		integer	type_p2,
		real( kind=4 ), intent(in)	dist,
		real( kind=8 ), intent(in)	mirror_z,
		real ( kind=8 ), intent(out)	energy2_partial
	)

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energy_partial_analytic_hom_charged_surf()

subroutine mod_compute_analytic_2proteins::energy_partial_analytic_hom_charged_surf	(	type(protein), intent(in)	prot1,
		type(protein), intent(in)	prot2,
		integer	type_p2,
		real(kind=4)	dist,
		real(kind=8), intent(out)	energy2_partial
	)

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force_analytic_dh()

subroutine mod_compute_analytic_2proteins::force_analytic_dh	(	type ( array_protein_type ), intent(in), target	tab_protein,
		type ( type_force_energy ), intent(in)	param_force_energy,
		real( kind=4 ), intent(in)	dist,
		real ( kind=8 ), dimension ( 3 ), intent(inout)	f,
		real ( kind=8 ), dimension ( 3 ), intent(inout)	t,
		real ( kind=8 ), dimension ( 3 ), intent(inout)	t1
	)

Compute force with analytic function.
Values precomputed and stored in an array Seems necessary to make separate for dh ? easier.

Parameters

tab_protein	: instance of array_protein_type
param_force_energy	: instance of type_force_energy
dist	: distance between solutes, in Angs.
f,t,t1	: force and torques on the solute 2, torque on 1

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force_analytic_dh_imgchg()

subroutine mod_compute_analytic_2proteins::force_analytic_dh_imgchg	(	type ( array_protein_type ), intent(in), target	tab_protein,
		type ( type_force_energy ), intent(in)	param_force_energy,
		real( kind=4 ), intent(in)	dist,
		real ( kind=8 ), dimension ( 3 ), intent(inout)	f,
		real ( kind=8 ), dimension ( 3 ), intent(inout)	t
	)

Compute forces for image charge DH routine NJB: Changed to move reflection plane to edge atomic layer when surface more than one atom.

Parameters

tab_protein	: mod_array_protein::array_protein_type to store solutes
param_force_energy	: mod_force_energy::type_force_energy describing forces etc
dist	: distance between solutes (ust z height with surface)
f	: force on mobile solute
t	: torque on mobile solute

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force_analytic_hom_charged_surf()

subroutine mod_compute_analytic_2proteins::force_analytic_hom_charged_surf	(	type ( array_protein_type ), intent(in), target	tab_protein,
		type ( type_force_energy ), intent(in)	param_force_energy,
		real( kind=4 ), intent(in)	dist,
		real ( kind=8 ), dimension ( 3 ), intent(inout)	f,
		real ( kind=8 ), dimension ( 3 ), intent(inout)	t
	)

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force_full_analytic_dh_imgchg()

subroutine mod_compute_analytic_2proteins::force_full_analytic_dh_imgchg	(	type ( protein ), intent(in)	prot2,
		integer, intent(in)	type_p2,
		real( kind=4 ), intent(in)	dist,
		real( kind=8 ), intent(in)	mirror_z,
		real ( kind=8 ), dimension ( 3 ), intent(out)	ff_analytic
	)

Convert to kT/A

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force_full_analytic_hom_charged_surf()

subroutine mod_compute_analytic_2proteins::force_full_analytic_hom_charged_surf	(	type ( protein ), intent(in)	prot1,
		type ( protein ), intent(in)	prot2,
		integer	type_p2,
		real( kind=4 ), intent(in)	dist,
		real ( kind=8 ), dimension ( 3 ), intent(out)	ff_analytic
	)

Convert to kT/A

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force_partial_analytic_dh_imgchg()

subroutine mod_compute_analytic_2proteins::force_partial_analytic_dh_imgchg	(	type ( protein ), intent(in)	prot2,
		integer, intent(in)	type_p2,
		real ( kind=4 ), intent(in)	dist,
		real ( kind=8 ), intent(in)	mirror_z,
		real ( kind=8 ), dimension ( 3 ), intent(out)	ff_partial,
		real ( kind=8 ), dimension ( 3 ), intent(out)	tt_partial
	)

Convert to kT/A

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force_partial_analytic_hom_charged_surf()

subroutine mod_compute_analytic_2proteins::force_partial_analytic_hom_charged_surf	(	type ( protein ), intent(in)	prot1,
		type ( protein ), intent(in)	prot2,
		integer	type_p2,
		real ( kind=4 )	dist,
		real ( kind=8 ), dimension ( 3 ), intent(out)	ff_partial,
		real ( kind=8 ), dimension ( 3 ), intent(out)	tt_partial
	)

Convert to kT/A

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pair_energy_full_analytic_2proteins()

subroutine mod_compute_analytic_2proteins::pair_energy_full_analytic_2proteins	(	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.
Need to split, cutoffs may be different/ asymetric between p1 and p2.
Only compute El-DH prot1 in analytical grid of protein 2 ( all grids stored in prot2 % p_sogrid % pset_analytical) Not good for 2 proteins because asymetry between static/mobil solute Need to test cutoffs for each interaction.

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

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pair_energy_partial_analytic()

subroutine mod_compute_analytic_2proteins::pair_energy_partial_analytic	(	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
	)

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

Parameters

prot1,prot2	: solute 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

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pair_force_full_analytic_2proteins()

subroutine mod_compute_analytic_2proteins::pair_force_full_analytic_2proteins	(	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 ), dimension ( 3 ), intent(out)	ff2,
		real ( kind=8 ), dimension ( 3 ), intent(out)	ff1
	)

Compute force if solute and grids do not overlap p2 solute in DH "grid" of p1, and opposite.
.

Parameters

prot1,prot2	: solute 1 (fixed) and 2 , instance of protein
type_p1,type_p2	: integer for the solute type
dist	: distance between the 2 solutes
ff2,ff1	: 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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pair_force_partial_analytic_2proteins()

subroutine mod_compute_analytic_2proteins::pair_force_partial_analytic_2proteins	(	type ( protein ), intent(in)	prot1,
		type ( protein ), intent(in)	prot2,
		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 is set to zero if inside the cutoff.

Parameters

prot1,prot2	: solute 1 and 2, instance of protein
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

Convert to kT/A

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