SDA  7.1
Simulation of Diffusional Association
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Functions/Subroutines
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_rotation (torque, rot_try, rot_displ, rmsang, prot_id)
 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)
 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 7.1 (2015)}

Copyright (c) 2009, 2010, 2015 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) formerly EML Research gGmbH (EML-R ) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Copyright (c) 2000, 2003 European Molecular Biology Laboratory Meyerhofstr. 1, Postfach 10.2209 D-69012, 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/doc/doc_sda7/references.html):

Brownian dynamics simulation of protein-protein diffusional encounter.

(1998) Methods, 14, 329-341.

Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, R.R.Gabdoulline, M. Ozboyaci, S.Richter and R.C.Wade


Function/Subroutine Documentation

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 
)

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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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 
)

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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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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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

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