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SDA (SDA flex)
7.2
Simulation of Diffusional Association
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SDA (SDA flex)
7.2
Simulation of Diffusional Association
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Data Types | |
| type | mod_analytic::analytic |
| Define tyoe analytic interactions (Debye-Huckel/crowders) More... | |
Modules | |
| module | mod_analytic |
| Analytical expressions, store energy and force in precomputed array. | |
Functions/Subroutines | |
| subroutine | mod_analytic::fill_array_dh (this, list_dh_radius) |
| subroutine | mod_analytic::set_zeroes (this, cutoff) |
| Specific to Debye-Huckel set zero for at distance where the grid is available Allow to call normal electrostatic and debye-huckel without taking care (hopefully) More... | |
| subroutine | mod_analytic::allocate_analytic (this) |
| Allocate the object with default values, arrays filled by param_force_energy:init_analytic when all data (cutoff,..) are known. More... | |
| subroutine | mod_analytic::deallocate_analytic (this) |
| Deallocate all analytic arrays. . More... | |
| subroutine | mod_analytic::set_analytic_params (this, h, max_size, epfct, dh_radius, vol_radius, rep_radius, surface_charge_dens, surf_prefct, gouy_chapman) |
| fill the arrays, here need to setup dimension More... | |
| subroutine | mod_analytic::set_dh_params (this, opt_ionic) |
| Initialize debye-huckel parameters. More... | |
| real(kind=8) function | mod_analytic::get_energy_analytic (this, bin, type_nb) |
| Return precomputed energy values. More... | |
| real(kind=8) function | mod_analytic::get_force_analytic (this, bin, type_nb) |
| Return precomputed force values. More... | |
| real(kind=8) function | mod_analytic::get_force_analytic_hom_charged_surf (this, bin, type_nb) |
| subroutine | mod_analytic::print_analytic (this) |
| Print values of array force and energy. Called by info_analytic. More... | |
| subroutine | mod_analytic::info_analytic (this, opt_print) |
| Print info about analytical grids. More... | |
| subroutine | mod_analytic::print_analytic_external (this) |
| subroutine | mod_analytic::print_analytic_external_hom_charged_surf (this) |
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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
Define analytical interactions, stored in 1D array
1.9.1
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