bd_move.f90 File Reference

Implement functions for BD translation and rotation, boost. More...

Functions/Subroutines
subroutine	bd_translation (rorig, cell, rtry, geom, force, dmd, rmsnow)
	Return a random vector for translation Used by both sda and sdamm PBC applied by update translation in mod_geometry Thread-safe function. More...
subroutine	bd_translation_surf_hydro (rorig, cell, rtry, geom, force, dmd_xy, dmd_z, rmsnow)
subroutine	bd_rotation (torque, rot_try, rot_displ, rmsang, prot_id, old_rotation)
	Return a random rotation matrix rot_try Function used by sda_2proteins, which corrects rotation of protein 1 into a translation of protein 2. More...
subroutine	bd_rotation_simple (torque, rot_try, rot_displ, rmsang, old_rotation)
	Return a random rotation matrix rot_try Simple version without correction. Used by sdamm. More...
subroutine	boost (r, geom, dist, rboost)
	Apply boost if too many overlaps, only for sda_2protein. More...

Detailed Description

Implement functions for BD translation and rotation, boost.

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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Function/Subroutine Documentation

bd_rotation()

subroutine bd_rotation	(	real ( kind=8 ), dimension(3), intent(in)	torque,
		real ( kind=8 ), dimension (3,3), intent(out)	rot_try,
		real ( kind=8 )	rot_displ,
		real ( kind=8 )	rmsang,
		integer, intent(in)	prot_id,
		logical	old_rotation
	)

Return a random rotation matrix rot_try
Function used by sda_2proteins, which corrects rotation of protein 1 into a translation of protein 2.

Parameters

torque	: torque between proteins
rot_try	: rotation after BD, matrix form
rot_displ	: rotational diffusion coefficient
rmsang	: fluctuation for rotation
prot_id	: index of the protein, if 1 apply the inverse transformation to protein 2

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bd_rotation_simple()

subroutine bd_rotation_simple	(	real ( kind=8 ), dimension (3), intent(in)	torque,
		real ( kind=8 ), dimension (3,3), intent(out)	rot_try,
		real ( kind=8 )	rot_displ,
		real ( kind=8 )	rmsang,
		logical	old_rotation
	)

Return a random rotation matrix rot_try
Simple version without correction. Used by sdamm.

Parameters

torque	: total torque on one protein
rot_try	: rotational BD in matrix form
rot_displ	: rotational coeffcient
rmsang	: fluctuation for rotation

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bd_translation()

subroutine bd_translation	(	real ( kind=8 ), dimension ( 3 ), intent(in)	rorig,
		integer, dimension ( 3 ), intent(inout)	cell,
		real ( kind=8 ), dimension ( 3 )	rtry,
		type ( geometry ), intent(in)	geom,
		real ( kind=8 ), dimension ( 3 ), intent(in)	force,
		real ( kind=8 ), intent(in)	dmd,
		real ( kind=8 ), intent(in)	rmsnow
	)

Return a random vector for translation
Used by both sda and sdamm
PBC applied by update translation in mod_geometry
Thread-safe function.

Parameters

rorig	: original position
cell	:
rtry	: position after translation
geom	: instance of mod_geometry
force	: force on the solute
dmd	: diffusional translation
rmsnow	: fluctuation term in translation

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bd_translation_surf_hydro()

subroutine bd_translation_surf_hydro	(	real ( kind=8 ), dimension ( 3 ), intent(in)	rorig,
		integer, dimension ( 3 ), intent(inout)	cell,
		real ( kind=8 ), dimension ( 3 )	rtry,
		type ( geometry ), intent(in)	geom,
		real ( kind=8 ), dimension ( 3 ), intent(in)	force,
		real ( kind=8 ), intent(in)	dmd_xy,
		real ( kind=8 ), intent(in)	dmd_z,
		real ( kind=8 ), intent(in)	rmsnow
	)

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boost()

subroutine boost	(	real ( kind=8 ), dimension( 3 )	r,
		type ( geometry ), intent(in)	geom,
		real ( kind=4 ), intent(in)	dist,
		real ( kind=4 ), intent(in)	rboost
	)

Apply boost if too many overlaps, only for sda_2protein.

Parameters

r	: relative position, updated buring the boost
geom	: instance of mod_geometry
dist	: distance before the boost
rboost	: boost value