mod_compute_energy_sdamm Module Reference

Module for computing energy, case sdamm. More...

Functions/Subroutines
subroutine	energy_epedhdlj_sdamm (tab_prot, geom, nb_prot, param_force_energy, array_energy, dummy_array)
	Compute multi proteins energy Loop over all pairs of proteins and interactions. More...
subroutine	compute_energy_sdamm_2proteins (prot1, prot2, pos_relat, grid_number, dummy_array, energy1, energy2, subgrid, type_p1, type_p2, test_dist2, skip_int)
	Compute the energy term for one interaction for a particular pair of solutes. . More...
subroutine	energy_epedhdlj_sdamm_fast (tab_prot, geom, nb_prot, param_force_energy, array_energy, dummy_array)
	Compute the energy for sdamm simualtions with the fast algorithm. More...
subroutine	compute_energy_couple_sdamm_fast (prot1, prot2, pos_relat, nb_grid1, nb_grid2, gridtype, dummy_array, energy11, energy12, energy21, energy22, type_p1, type_p2, test_dist2)
	Compute a couple of interaction at once . More...

Detailed Description

Module for computing energy, case sdamm.

Function/Subroutine Documentation

compute_energy_couple_sdamm_fast()

subroutine mod_compute_energy_sdamm::compute_energy_couple_sdamm_fast	(	type ( protein ), intent(in)	prot1,
		type ( protein ), intent(in)	prot2,
		real ( kind=8 ), dimension ( 3 ), intent(in)	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 ), intent(out)	energy11,
		real ( kind=8 ), intent(out)	energy12,
		real ( kind=8 ), intent(out)	energy21,
		real ( kind=8 ), intent(out)	energy22,
		integer, intent(in)	type_p1,
		integer, intent(in)	type_p2,
		real (kind=4), intent(in)	test_dist2
	)

Compute a couple of interaction at once
.

Can compute electrostatic/desolvation or hydrophobic/ repulsive lennard-jones at the same time Need all symetric interaction.

Parameters

prot1	: solute 1
prot2	: solute 2
pos_relat	: position relative after PBC
nb_grid1	: grid to use for interaction 1
nb_grid2	: grid to use for interaction 2
gridtype	: type of the couple of grids (1 = Ep/Des or 2 == Hd/RepLj )
dummy_array	: : used for the computation of repulsive lennard-jones interaction
energy11	: energy of protein 1 in the grid of protein 2 ( with type grid 1 )
energy12	: energy of protein 1 in the grid of protein 2 ( with type grid 2 )
energy21	: energy of protein 2 in the grid of protein 1 ( with type grid 1 )
energy22	: energy of protein 2 in the grid of protein 1 ( with type grid 2 )
type_p1,type_p2	: integer type of the solutes
test_dist2	: distance square between the solutes

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compute_energy_sdamm_2proteins()

subroutine mod_compute_energy_sdamm::compute_energy_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)	dummy_array,
		real ( kind=8 ), intent(out)	energy1,
		real ( kind=8 ), intent(out)	energy2,
		integer, intent(in)	subgrid,
		integer, intent(in)	type_p1,
		integer, intent(in)	type_p2,
		real (kind=4), intent(in)	test_dist2,
		integer, intent(in)	skip_int
	)

Compute the energy term for one interaction for a particular pair of solutes.
.

Explicit tests are done to check asymetry

Parameters

prot1	: solute 1
prot2	: solute 2
pos_relat	: relative position between the 2 proteins
grid_number	: specify the type of interaction
dummy_array	: used for the computation of repulsive lennard-jones interaction
energy1	: return energy of protein 1 in the grid of protein 2
energy2	: return energy of protein 2 in the grid of protein 1
subgrid	: subgrid number (only LJ now)
type_p1,type_p2	: integer type of the solutes
test_dist2	: distance square between the solutes

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energy_epedhdlj_sdamm()

subroutine mod_compute_energy_sdamm::energy_epedhdlj_sdamm	(	type ( array_protein_type ), target	tab_prot,
		type ( geometry )	geom,
		integer	nb_prot,
		type ( type_force_energy ), intent(in)	param_force_energy,
		real ( kind=8 ), dimension( :, :), intent(out)	array_energy,
		real ( kind=8 ), dimension( : )	dummy_array
	)

Compute multi proteins energy
Loop over all pairs of proteins and interactions.

Parameters

tab_prot	: array with all solutes
geom	: instance of mod_geometry
nb_prot	: total number of solutes
param_force_energy	: instance type_force_energy in mod_force_energy
dummy_array	: used for the computation of repulsive lennard-jones interaction
array_energy	: return, to store energies

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energy_epedhdlj_sdamm_fast()

subroutine mod_compute_energy_sdamm::energy_epedhdlj_sdamm_fast	(	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)	array_energy,
		real ( kind = 8 ), dimension ( : ), intent(in)	dummy_array
	)

Compute the energy for sdamm simualtions with the fast algorithm.

If couple_grid is not used, asymetry is treated. ( see limitation with 2 asymetric grids )

Include 2 cut-offs, one between proteins ( use distance ) and one between a surface and the proteins ( use z-distance )
Same than fast for force, delete the loop over the grids and compute rotation of "charge" only once

Parameters

tab_prot	: array with all solutes
geom	: instance of mod_geometry
nb_prot	: total number of solutes
param_force_energy	: instance of type_force_energy
dummy_array	: used for the computation of repulsive lennard-jones interaction
array_energy	: return, to record energies

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