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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_residencetime::residence_time |
| Arrays for 1, 2 and 3 dimensional residence time and radial distribution function with sdamm. More... | |
Modules | |
| module | mod_residencetime |
| residence time and rdf statistics | |
Functions/Subroutines | |
| subroutine | mod_residencetime::init_resid_time (this, fixe_bin_size, enum_str, format_resid3d, b_pair, nb_type) |
| Initialize the instance. More... | |
| subroutine | mod_residencetime::delete_resid_time (this) |
| Delete arrays. More... | |
| subroutine | mod_residencetime::copy_resid_time (this, new_rt, new_enum_rt) |
| Not a real copy, data are modified when we want to create a 2D or a 1D form a 3D reisdence_time. More... | |
| subroutine | mod_residencetime::set_array_rt (this, geom_resid, nb_xcell, nb_ycell, nb_zcell, xcell, ycell, zcell) |
| Set grid parameters. More... | |
| subroutine | mod_residencetime::set_array_rt_sdamm (this, geom_resid, nb_type, nb_xcell, nb_ycell, nb_zcell, xcell, ycell, zcell) |
| Similar to set_array_rt but only for sdamm. More... | |
| subroutine | mod_residencetime::apply_shift_to_rt (this, shift_x, shift_y, shift_z) |
| Shift the origin of the residence_time grid. More... | |
| subroutine | mod_residencetime::update_residence_time (this, pos_prot, dist, dtnow) |
| Update residence_time. More... | |
| subroutine | mod_residencetime::update_rdf (this, dist, type1, type2) |
| Update the radial distribution function. More... | |
| recursive integer function | mod_residencetime::print_residence_time (this, geom_resid, nrun) |
| Print final residence_time. More... | |
| subroutine | mod_residencetime::print_rdf (this, tab_protein, geom_resid, n_rdfs) |
| Normalize and print radial distribution functions in RDF.log. More... | |
| subroutine | mod_residencetime::write_resid_3d (this, shift_center) |
| Write the 3d reisdence time grid to UHBD format. More... | |
Variables | |
| integer, parameter | mod_residencetime::rt_off = 1 |
| integer, parameter | mod_residencetime::rt_distance = 2 |
| integer, parameter | mod_residencetime::rt_plan = 3 |
| integer, parameter | mod_residencetime::rt_resid3d = 4 |
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
Compute, store and print all residence time and the radial distribution function with sdamm
1.9.1
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