mod_flexibility.f90 File Reference

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

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

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

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Allow the change in conformation of the solutes

Subroutines in change_conformation.f90 implement the different algorithms.