make_edhdlj_grid.f90 File Reference

Functions/Subroutines
program	make_edhdlj_grid
	Prgram make_edhdlj_grid.
subroutine	read_input (name_input, grid_type, parameters)
	Read specific input file for the grids.
subroutine	compute_ed (grid, list_atom, a2, a3, parameters)
	Compute electrostatic desolvation.
subroutine	compute_hd (grid, list_atom, array_van, parameters, opt_pdb, opt_omit_pdb)
	Compute apolar desolvation.
subroutine	compute_ljrep (grid, list_atom, array_van, parameters)
	Compute soft-core (repulsive lennard-jones)
subroutine	dipole (list_atom, a2, a3, grid_pos, parameters, energy)
	Used for electrostic desovaltion computation.
subroutine	hdenergy (list_atom, grid_pos, array_van, parameters, energy, opt_pdb, opt_omit_pdb)
	Use for apolar desolvation computation.
subroutine	ljrep_energy (list_atom, array_van, grid_pos, parameters, energy)
	Use for repulsive lennard-jones computation.

Detailed Description

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

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Create electrostatic desolvation, apolar desolvation and repulsive lennard-jones grids

Function/Subroutine Documentation

compute_ed()

subroutine compute_ed	(	type ( type_grid )	grid,
		real ( kind = 8 ), dimension ( :, : ), intent(in)	list_atom,
		real ( kind=8 ), dimension ( : )	a2,
		real ( kind=8 ), dimension ( : )	a3,
		type ( param_list_tools ), intent(in)	parameters
	)

Compute electrostatic desolvation.

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compute_hd()

subroutine compute_hd	(	type ( type_grid )	grid,
		real ( kind = 8 ), dimension ( :, : ), intent(in)	list_atom,
		real ( kind = 8 ), dimension ( : ), intent(in)	array_van,
		type ( param_list_tools ), intent(in)	parameters,
		type ( type_pdb_file ), optional	opt_pdb,
		type ( type_pdb_file ), optional	opt_omit_pdb
	)

Compute apolar desolvation.

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compute_ljrep()

subroutine compute_ljrep	(	type ( type_grid )	grid,
		real ( kind = 8 ), dimension ( :, : ), intent(in)	list_atom,
		real ( kind = 8 ), dimension ( : ), intent(in)	array_van,
		type ( param_list_tools ), intent(in)	parameters
	)

Compute soft-core (repulsive lennard-jones)

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dipole()

subroutine dipole	(	real ( kind = 8 ), dimension ( :, : ), intent(in)	list_atom,
		real ( kind=8 ), dimension ( : ), intent(in)	a2,
		real ( kind=8 ), dimension ( : ), intent(in)	a3,
		real ( kind=8 ), dimension ( 3 ), intent(in)	grid_pos,
		type ( param_list_tools ), intent(in)	parameters,
		real ( kind=8 ), intent(out)	energy
	)

Used for electrostic desovaltion computation.

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hdenergy()

subroutine hdenergy	(	real ( kind = 8 ), dimension ( :, : ), intent(in)	list_atom,
		real ( kind=8 ), dimension ( 3 ), intent(in)	grid_pos,
		real ( kind = 8 ), dimension ( : ), intent(in)	array_van,
		type ( param_list_tools )	parameters,
		real ( kind=8 ), intent(out)	energy,
		type ( type_pdb_file ), optional	opt_pdb,
		type ( type_pdb_file ), optional	opt_omit_pdb
	)

Use for apolar desolvation computation.

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ljrep_energy()

subroutine ljrep_energy	(	real ( kind = 8 ), dimension ( :, : ), intent(in)	list_atom,
		real ( kind = 8 ), dimension ( : ), intent(in)	array_van,
		real ( kind=8 ), dimension ( 3 ), intent(in)	grid_pos,
		type ( param_list_tools ), intent(in)	parameters,
		real ( kind=8 ), intent(out)	energy
	)

Use for repulsive lennard-jones computation.

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read_input()

subroutine read_input	(	character *128, intent(in)	name_input,
		integer, intent(in)	grid_type,
		type ( param_list_tools ), intent(out)	parameters
	)

Read specific input file for the grids.

Parameters

name_input	: file name of the input
grid_type	: integer for the grid_type, refer to mod_gridtype
parameters	: specific parameters for tools param_list_tools

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