mod_setofgrid.f90 File Reference

Data Types
type	mod_setofgrid::sogrid
	Store all grids ( UHBD type), and "charges": charges, accessibility and their position. More...

Modules
module	mod_setofgrid
	Module for storing data needed for a specific conformation. store all grids and position of atoms.

Functions/Subroutines
subroutine	mod_setofgrid::allocate_sogrid (this)
	Initialze sogrid with the total number of grid declared in mod_gridtype.f90.
subroutine	mod_setofgrid::delete_sogrid (this)
	Delete sogrid.
subroutine	mod_setofgrid::load_grid (this, filename, t_grid, scfct_opt, iform_opt)
	Load one grid or one "charge", can read binary or ascii format Add analytical interactions ( negative grid number ).
subroutine	mod_setofgrid::load_ljgrid (this, type_to_load, lj_filename, pdb_filename, opt_fct)
	allocate and load lj_grid, should be done only once need more option, only one of lj / atom should be allocated keep one function, need type_to_load : 1 or 2, both are array of characters
subroutine	mod_setofgrid::set_analytic (this, name_type, list_rad, bin_size, max_size, surf_prefct, gouy_chapman, opt_extra_param)
	Initialize one analytic array.
subroutine	mod_setofgrid::set_sphere_crowder (this, array_dh_rad, array_rep_rad, ionic, rep_bfct, h_size, max_dist)
subroutine	mod_setofgrid::allocate_charge (this, nat)
	Allocate charge array and square of the charges for electrostatic desolvation.
subroutine	mod_setofgrid::allocate_acc_surf (this, nat2)
	Allocate accessibility and list_atom_surface array.
subroutine	mod_setofgrid::read_charge (this, echa_filename)
	Function to read charges, and make charge_square.
real(kind=8) function	mod_setofgrid::get_max_debye (this)
	Used ??
subroutine	mod_setofgrid::write_accessibility (this, access_filename, center_prot, vdw, max_vdw, max_dist, param_probe)
	Write acceessibility into a file.
subroutine	mod_setofgrid::read_accessibility (this, access_filename, center_prot, vdw, max_vdw, max_dist, param_probe, opt_recalculate)
	Read accessibility file.
subroutine	mod_setofgrid::read_sasa_pdb (this, sasa_filename, vdw)
	Read sasa_pdb file.
subroutine	mod_setofgrid::set_ofgrid_info (this)
	Print info of this set_of_grid.

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, A.Muñiz-Chicharro, R.Beccaria 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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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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store all grids and position of atoms