SDA (SDA flex)  7.2
Simulation of Diffusional Association
Data Types | Modules | Functions/Subroutines
mod_protein.f90 File Reference

Data Types

type  mod_protein::protein
 Define properties of one solute / protein. More...


module  mod_protein
 Module to define one protein (position, orientation, is surface?)


subroutine mod_protein::new_protein (this, irot, isurf, iflex, iimg_chg, id, vert_excl, opt_imdesolv)
 Allocate one protein. More...
subroutine mod_protein::set_flexible (this, plist_flexible)
 Allocate a flexible and assign the plist_flexible. More...
subroutine mod_protein::allocate_array_mdesolv (this, param_metaldesolv)
subroutine mod_protein::delete_protein (this)
 Destructor, normally not called directly but by mod_array_protein add new variable local_copy, simpler and allow easier for flex. More...
subroutine mod_protein::update_rot_orientation (this, mrot)
 rotate orientation axis version with explicit terms, faster More...
subroutine mod_protein::update_rotation_protein (this, matrix_rot)
 Rotate the position of atoms/ charges / etc. version with explicit rotation, faster now use the pointer, either points to a sogrid copy, or rotate the local copy. More...
subroutine mod_protein::info_protein (this)
 Print info. More...
subroutine mod_protein::init_movable_array (this, sgrid, make_local_copy)
 Make the copy of the atomic position to protein if make_local_copy is true Otherwise points to sogrid why sgrid ? already associated ? Not if flex to check. More...
subroutine mod_protein::copy_movable_array (this, opt_mat)
 Copy movable atoms from sogrid arrays to a local copy in the protein. Needed in case of flexibility (keep a copy of the initial position), certianly sda_pmf (with option opt_mat)\ Check if local copy is true, otherwise do nothing
Optional opt_mat will load the initial position locally and apply the matrix of rotation.
. More...
subroutine mod_protein::select_charge (grid_number, prot1, prot2, nq1, nq2, p_charge1, p_charge2, p_charge_position1, p_charge_position2, dummy_array)
 First version, fastest version, do not check for asymetry.
. More...
subroutine mod_protein::select_charge2 (grid_number, prot1, prot2, nq1, nq2, p_charge1, p_charge2, p_charge_position1, p_charge_position2, dummy_array, opt_pgrid1, opt_pgrid2, opt_subgrid)
 Select correct pointer for charges ( and optionaly subgrids : only lennard-jones now ).
. More...
subroutine mod_protein::initialize_conformation (this, opt_conf_nb)
 Initialize the conformation in case of flexible.
replace change_conformation::init_conformation
. More...
subroutine mod_protein::update_visited_conf (this, timestep)
 update array statistics for sda_flex, use timestep rather than integer, may change More...
subroutine mod_protein::merge_visited_conf (this, to_merge)
subroutine mod_protein::print_visited_conf (this)

Detailed Description

{version 7.2.3 (2019)}

Copyright (c) 2009, 2010, 2015, 2016, 2019 Heidelberg Institute of Theoretical Studies (HITS, Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

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References: see also

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 one protein or solute