mod_protein.f90 File Reference

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

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

Functions/Subroutines
subroutine	mod_protein::new_protein (this, irot, isurf, iflex, iimg_chg, id, vert_excl, opt_imdesolv)
	Allocate one protein.
subroutine	mod_protein::set_flexible (this, plist_flexible)
	Allocate a flexible and assign the plist_flexible.
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.
subroutine	mod_protein::update_rot_orientation (this, mrot)
	rotate orientation axis version with explicit terms, faster
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.
subroutine	mod_protein::info_protein (this)
	Print info.
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.
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. .
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. .
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 ). .
subroutine	mod_protein::initialize_conformation (this, opt_conf_nb)
	Initialize the conformation in case of flexible. replace change_conformation::init_conformation .
subroutine	mod_protein::update_visited_conf (this, timestep)
	update array statistics for sda_flex, use timestep rather than integer, may change
subroutine	mod_protein::merge_visited_conf (this, to_merge)
subroutine	mod_protein::print_visited_conf (this)

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, A.Muñiz-Chicharro, R.Beccaria 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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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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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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Define one protein or solute