mod_compute_pmf Module Reference

Functions/Subroutines
subroutine	main_pmf (tab_protein, param_force_energy, mentx, menty, mentth, mentfi, mentom, ent, surf_atoms, charge_points, cmx, dx, dy, dt, erotnorm, energymin, irtst, ds, dz, wz, pz, sz, dist, dummy_array, param_metaldesolv, type_calc, o_complexes)
	Main subroutine to compute the pmf in each dZ distance above the surface. Called by MainLoop_sda_energy.f90.
subroutine	comp_pmf (ent, mentth, mentfi, mentom, mentx, menty, ds, wz, pz, sz, erotnorm, istp)
	Subroutine to compute the pmf value for a given z above the surface. rotational and translation configurational distributions c and write occupation map (translational and rotational) norm to 1; dV=dT*dz- 3-dimentional space volume = zmax*4pi.
subroutine	rotation_pmf (rot, rotentfi, rotentth, rotentom)
	compute the rotation matrix for a given set of angles.
subroutine	update_rotation_pmf (prot2, matrix_rot, surf_atoms, charge_points)
	get new protein axis and atoms coordinate after rotation and update.

Function/Subroutine Documentation

comp_pmf()

subroutine mod_compute_pmf::comp_pmf	(	real ( kind=8 ), dimension (:,:,:,:,:), intent(in)	ent,
		integer, intent(in)	mentth,
		integer, intent(in)	mentfi,
		integer, intent(in)	mentom,
		integer, intent(in)	mentx,
		integer, intent(in)	menty,
		real ( kind=8 ), intent(in)	ds,
		real ( kind=8 ), intent(inout)	wz,
		real ( kind=8 ), intent(inout)	pz,
		real ( kind=8 ), intent(inout)	sz,
		real ( kind=8 ), intent(in)	erotnorm,
		integer, intent(inout)	istp
	)

Subroutine to compute the pmf value for a given z above the surface.
rotational and translation configurational distributions c and write occupation map (translational and rotational) norm to 1; dV=dT*dz- 3-dimentional space volume = zmax*4pi.

ppp*dT*dZ is the probability of finding the protein at Y+dT, Z+dZ DH- change of enthalpy, DSt - change of translational entropy; DSr- rot entropy

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main_pmf()

subroutine mod_compute_pmf::main_pmf	(	type ( array_protein_type ), intent(inout), target	tab_protein,
		type ( type_force_energy ), intent(in)	param_force_energy,
		integer, intent(in)	mentx,
		integer, intent(in)	menty,
		integer, intent(in)	mentth,
		integer, intent(in)	mentfi,
		integer, intent(in)	mentom,
		real ( kind=8 ), dimension (:,:,:,:,:), intent(inout)	ent,
		real ( kind=8 ), dimension (:,:), intent(inout)	surf_atoms,
		real ( kind=8 ), dimension (:,:), intent(inout)	charge_points,
		real ( kind=8 ), dimension (15), intent(inout)	cmx,
		real ( kind=8 ), intent(in)	dx,
		real ( kind=8 ), intent(in)	dy,
		real ( kind=8 ), intent(inout)	dt,
		real ( kind=8 ), intent(inout)	erotnorm,
		real ( kind=8 ), intent(out)	energymin,
		integer, intent(inout)	irtst,
		real ( kind=8 ), intent(in)	ds,
		real ( kind=8 ), intent(in)	dz,
		real ( kind=8 ), intent(out)	wz,
		real ( kind=8 ), intent(out)	pz,
		real ( kind=8 ), intent(out)	sz,
		real ( kind=4 ), intent(in)	dist,
		real ( kind = 8 ), dimension ( : ), intent(in)	dummy_array,
		type ( parameter_metaldesolv )	param_metaldesolv,
		type ( type_calculation ), intent(in)	type_calc,
		type ( record ), intent(in)	o_complexes
	)

Main subroutine to compute the pmf in each dZ distance above the surface.
Called by MainLoop_sda_energy.f90.

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rotation_pmf()

subroutine mod_compute_pmf::rotation_pmf	(	real ( kind=8 ), dimension ( 3,3 ), intent(inout)	rot,
		real ( kind=8 ), intent(in)	rotentfi,
		real ( kind=8 ), intent(in)	rotentth,
		real ( kind=8 ), intent(in)	rotentom
	)

compute the rotation matrix for a given set of angles.

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update_rotation_pmf()

subroutine mod_compute_pmf::update_rotation_pmf	(	type ( protein ), intent(inout)	prot2,
		real ( kind=8 ), dimension(3,3), intent(in)	matrix_rot,
		real ( kind=8 ), dimension (:,:), intent(in)	surf_atoms,
		real ( kind=8 ), dimension (:,:), intent(in)	charge_points
	)

get new protein axis and atoms coordinate after rotation and update.

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