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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_flexibility::nodeflex |
| Define nodes of list_flex, internal use. More... | |
| type | mod_flexibility::list_flex_type |
| List of set of grid. More... | |
| type | mod_flexibility::flexible |
| Main class owned by each protein to allow a change in conformation. More... | |
Modules | |
| module | mod_flexibility |
| Module for flexibility. | |
Functions/Subroutines | |
| subroutine | mod_flexibility::new_flexible (this, plist_flex) |
| Constructor flexible . More... | |
| subroutine | mod_flexibility::delete_flexible (this) |
| Destructor flexible. More... | |
| subroutine | mod_flexibility::init_flexible_freq (this) |
| Initialize or reinitialze the time for the next change in conformation : time_next_flex. More... | |
| subroutine | mod_flexibility::new_list_flex (this, flex_method_str, list_conf_fname, total_conf, initial_conf, nearest_ngb, frequence, std_freq) |
| Constructor of list_flexible. More... | |
| subroutine | mod_flexibility::delete_listflex (this) |
| Delete the full list and the associated sogrid. More... | |
| subroutine | mod_flexibility::delete_last_dataflex (this, status) |
| Deleta the last node of the list and the associated sogrid. More... | |
| subroutine | mod_flexibility::delete_first_dataflex (this, status) |
| not used until now, to delete ?? More... | |
| subroutine | mod_flexibility::insert_sogrid (this, p_sogrid, head, status) |
| Insert a new sogrid and create a new node. More... | |
| recursive integer function | mod_flexibility::associate_to_conformation (this, pnew_node, nb_conf, counter, shift_conf) |
| Associate pointer pnew_node to the conformation number. More... | |
| subroutine | mod_flexibility::change_conf_flex (this, conf_nb, shift_conf_opt) |
| Update the p_current_node of flex to conformation nb_conf (== -1 random ) or shift_conf ( +/- 1 ) More... | |
Variables | |
| integer, parameter | mod_flexibility::flex_intern = 0 |
| enumeration of node's state for the list More... | |
| integer, parameter | mod_flexibility::flex_first = 1 |
| integer, parameter | mod_flexibility::flex_last = 2 |
| integer, parameter | mod_flexibility::flex_random = 0 |
| enumeration for the algorithm More... | |
| integer, parameter | mod_flexibility::flex_metropolis = 1 |
| integer, parameter | mod_flexibility::flex_minimum = 2 |
| integer, parameter | mod_flexibility::flex_time = 3 |
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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
Allow the change in conformation of the solutes
Subroutines in change_conformation.f90 implement the different algorithms.
1.9.1
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