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. More... | |
Compute the exclusion grid, only for sda_2proteins and solute 1.
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References (see also http://mcm.h-its.org/sda7/doc/doc_sda7/references.html):
Brownian dynamics simulation of protein-protein diffusional encounter.
(1998) Methods, 14, 329-341.
Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, R.R.Gabdoulline, M. Ozboyaci, S.Richter and R.C.Wade
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.
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 |