make_exclusion_grid.f90 File Reference

Compute the exclusion grid, only for sda_2proteins and solute 1. More...

Functions/Subroutines
subroutine	make_exclusion_grid (sgrid, tmp_atom_pos, tmp_nat, center, atom_vdw, max_vdw, probep, hexclusion)
	Use intermediate module mod_exclusion_grid.

Detailed Description

Compute the exclusion grid, only for sda_2proteins and solute 1.

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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Function/Subroutine Documentation

make_exclusion_grid()

subroutine make_exclusion_grid	(	type ( sogrid )	sgrid,
		real ( kind=8 ), dimension ( :, : )	tmp_atom_pos,
		integer	tmp_nat,
		real ( kind=8 ), dimension ( 3 )	center,
		real ( kind=8 ), dimension(:)	atom_vdw,
		real ( kind=8 )	max_vdw,
		real ( kind=4 )	probep,
		real ( kind=4 )	hexclusion
	)

Use intermediate module mod_exclusion_grid.

The grid is stored in a sogrid object, like all properties belonging to the protein conformation
It is stored as an UHBD grid. It can be written to file and visualised
Use probep the protein probe.

Parameters

sgrid	: instance of sogrid
tmp_atom_pos	: position of the atom
tmp_nat	: total number of atoms
center	: center of the solute ( used as input here ?? )
atom_vdw	: list of Van der Walls parameters for all atoms
max_vdw	: maximum value
probep	: protein probe
hexclusion	: size of cells for the exclusion grid

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