mod_set_parameters.f90 File Reference

Modules
module	mod_set_parameters
	Group functions to compute the cutoff, allocate dummy_array and energy array. used by all types of simulations.

Functions/Subroutines
subroutine	mod_set_parameters::set_dummy_array_and_logical (tab_protein, dummy_array, iflex)
	General function to setup the dummy_array and logical variable lennard-jones is missing here.
subroutine	mod_set_parameters::set_array_energy (type_calc, o_record, nb_prot, array_energy, opt_max_energy_terms, opt_size_array_energy, opt_force_large_array)
subroutine	mod_set_parameters::set_rhit (tab_prot, param_probe, rhit)
	To compute rhit, maximum distance where we need to check for overlap. .
subroutine	mod_set_parameters::set_cut_array (tab_protein, geom, cut2_max)
	Routine to generate an interaction cut off specific to each grid type. .
subroutine	mod_set_parameters::alloc_fill_cut_array (tab_protein, cur_sogrid, cur_prot)
	Routine to allocate and fill a grid specific cut off array for each solute/conformation.
subroutine	mod_set_parameters::set_hi_rad (tab_protein, geom, input_rad, hi_rad)
	Routine to find the Rcut value. – This is the radius used to define local volume in mean-field hydrodynamic approach. – At present, it finds the largest vol_radius of any solute, and multiplies this by a factor. – Does not use factor any more. Radius set in input file. This routine now just checks that chosen radius is larger than the largest vol_radius of any solute.

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

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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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Group the setting of cutoff, rhit ( distance for overlap testing), array of energies and dummy_array (used by all simulations)