trans_diffusion.f90 File Reference

Compute the autocorrelation function and translational diffusion coefficients. More...

Functions/Subroutines
program	trans_diffusion
	Program trans_diffusion. More...
subroutine	all_msd_translation (position, tab_prot, ACF, nchunks, b_type, value_type, nb_region, dt, io_dt)
	Compute all msd, autocorrelation function of the position. More...
subroutine	msd_translat (input_data, output_data)
	Version using the maximum number of data points. More...
subroutine	print_acftrans_sdamm (ACF, time_snapshot, b_type, value_type)
	Version with output similar to sdamm, need to produce more files. More...

Detailed Description

Compute the autocorrelation function and translational diffusion coefficients.

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

all_msd_translation()

subroutine all_msd_translation	(	real ( kind=8 ), dimension (:,:,:), intent(in)	position,
		type ( array_protein_type ), intent(in)	tab_prot,
		real ( kind=8 ), dimension (:,:,:), allocatable	ACF,
		integer, intent(in)	nchunks,
		logical, intent(in)	b_type,
		integer, intent(in)	value_type,
		integer, intent(in)	nb_region,
		real ( kind=4 ), intent(in)	dt,
		integer, intent(in)	io_dt
	)

Compute all msd, autocorrelation function of the position.

Parameters

position	: 3 dimensional array ( x, y, z, nb_prot, time ) with the position of the solutes
tab_prot	: instance of array_protein_type
ACF	: return, all autocorrelation function
nchunks	: number of part the trajectory must be split
b_type	: logical, compute for different type of proteins if .true.
value_type	if 0 compute for all proteins AND for all types of proteins, if > 0 compute only for this type, could improve, read in orient_axis only for this type and forget about this argument
nb_region	: number of regions ??
dt	: timestep
io_dt	: file descriptor for output

Here is the call graph for this function:

msd_translat()

subroutine msd_translat	(	real ( kind=8 ), dimension (:,:,:), intent(in)	input_data,
		real ( kind=8 ), dimension (:), intent(out)	output_data
	)

Version using the maximum number of data points.

Large tau values have a poor statistic

Parameters

input_data	: position of the solute
output_data	: autocorrelation function, 1 dimensional array

print_acftrans_sdamm()

subroutine print_acftrans_sdamm	(	real ( kind=8 ), dimension (:,:,:), intent(in)	ACF,
		real (kind=4)	time_snapshot,
		logical	b_type,
		integer	value_type
	)

Version with output similar to sdamm, need to produce more files.

For use with octave and rotation, here not used !!