ecm_mainsubroutine.f90 File Reference

Functions/Subroutines
subroutine	sub_mksites (filename, out_fname)
	sub_mksites, make the test charges More...
subroutine	sub_expand (list_param_ecm)
	sub_expand More...
subroutine	sub_regularize (a0, qT, q0, list_param_ecm, norm_grid)
	Make the regularization procedure. More...
subroutine	make_skin (grid, excl_grid, skin_grid, list_param_ecm)
	Create skin around the solute Called 2 times make_one_skin with different parameters to define a skin around the solute. More...
subroutine	make_one_skin (grid, list_param_ecm, natoms, nb_points, excl_grid, skin_grid, bool_first)
	make_one_skin need to re read pdb, because van argument Second call probsk is increased by skin More...
subroutine	rearra (grid, skin_grid, grid_linear, iar, jar, kar)
	Rearrange. keep only points where skin_grid is 1, put it in a unidimensional array. More...
subroutine	overlapping (grida, gridb, over)
	Compute the overlapping. More...
subroutine	coulomb (coul, tmp_pos, iar, jar, kar, grid, nb_points, fact, deb)
	Coulomb terms. More...

Function/Subroutine Documentation

coulomb()

subroutine coulomb	(	real ( kind=8 ), dimension ( nb_points )	coul,
		real ( kind=8 ), dimension ( 3 )	tmp_pos,
		integer (kind=8), dimension ( nb_points ), intent(in)	iar,
		integer (kind=8), dimension ( nb_points ), intent(in)	jar,
		integer (kind=8), dimension ( nb_points ), intent(in)	kar,
		type ( type_grid ), intent(in)	grid,
		integer( kind=8), intent(in)	nb_points,
		real ( kind=8 ), intent(in)	fact,
		real ( kind=8 ), intent(in)	deb
	)

Coulomb terms.

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make_one_skin()

subroutine make_one_skin	(	type ( type_grid ), intent(in)	grid,
		type ( param_ecm ), intent(in)	list_param_ecm,
		integer	natoms,
		integer	nb_points,
		integer ( kind=1 ), dimension ( :,:,: ), allocatable	excl_grid,
		integer ( kind=1 ), dimension ( :,:,: ), allocatable	skin_grid,
		logical	bool_first
	)

make_one_skin need to re read pdb, because van argument Second call probsk is increased by skin

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make_skin()

subroutine make_skin	(	type ( type_grid ), intent(in)	grid,
		integer ( kind=1 ), dimension ( :,:,: ), allocatable	excl_grid,
		integer ( kind=1 ), dimension ( :,:,: ), allocatable	skin_grid,
		type ( param_ecm )	list_param_ecm
	)

Create skin around the solute Called 2 times make_one_skin with different parameters to define a skin around the solute.

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overlapping()

subroutine overlapping	(	real ( kind=8 ), dimension ( : ), intent(in)	grida,
		real ( kind=8 ), dimension ( : ), intent(in)	gridb,
		real ( kind= 8 ), intent(out)	over
	)

Compute the overlapping.

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rearra()

subroutine rearra	(	type ( type_grid ), intent(in)	grid,
		integer ( kind=1 ), dimension (:,:,:), intent(in)	skin_grid,
		real ( kind=8 ), dimension ( : ), intent(out)	grid_linear,
		integer (kind=8), dimension ( : ), intent(out)	iar,
		integer (kind=8), dimension ( : ), intent(out)	jar,
		integer (kind=8), dimension ( : ), intent(out)	kar
	)

Rearrange.
keep only points where skin_grid is 1, put it in a unidimensional array.

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sub_expand()

subroutine sub_expand

(

type ( param_ecm )

list_param_ecm

)

sub_expand

Use for effective charge determination

Parameters

list_param_ecm

: parameters for ecm, defined in param_ecm

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sub_mksites()

subroutine sub_mksites	(	character, dimension(*), intent(in)	filename,
		character, dimension(*), intent(in)	out_fname
	)

sub_mksites, make the test charges

Version

{version 7.2.3 (2019)}

Copyright (c) 2009, 2010, 2015, 2016, 2019 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Please send your contact address to get information on updates and new features to "mcmsoft@h-its.org". Questions will be answered as soon as possible.

References: see also http://mcm.h-its.org/sda7/do:c/doc_sda7/references.html:

Brownian dynamics simulation of protein-protein diffusional encounter. (1998) Methods, 14, 329-341.

SDA 7: A modular and parallel implementation of the simulation of diffusional association software. Journal of computational chemistry 36.21 (2015): 1631-1645.

Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, X. Yu, M. Ozboyaci, M. Reinhardt, P. Friedrich, R.R.Gabdoulline, S.Richter and R.C.Wade

---

For ecm_mksites   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

make independent routine, can be called by ecm_all

Make the test charges

Parameters

filename	: pdb file to read atom types
out_fname	: file containing the test charges ( *.tcha )

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sub_regularize()

subroutine sub_regularize	(	real ( kind=8 ), dimension (:,:), intent(in)	a0,
		real ( kind=8 ), dimension (:), intent(in)	qT,
		real ( kind=8 ), dimension (:), intent(in)	q0,
		type ( param_ecm ), intent(in)	list_param_ecm,
		real ( kind=8 ), intent(in)	norm_grid
	)

Make the regularization procedure.

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