init_time.f90 File Reference

Functions/Subroutines
subroutine	init_time (param_timestep, geom, dist, rhit, dm30, dtnow, hit)
	Define instantaneous timestep if it is variable ( only for sda_2proteins ) . More...
subroutine	check_timestep (geom, param_timestep, tab_protein)
	Compute basic property about the maximum timestep... More...

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, 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 the timestep ( variable for sda_2proteins )

Function/Subroutine Documentation

check_timestep()

subroutine check_timestep	(	type ( geometry )	geom,
		type ( parameter_timestep )	param_timestep,
		type ( array_protein_type )	tab_protein
	)

Compute basic property about the maximum timestep...

Parameters

geom	: instance of mod_geometry
param_timestep	: structure for the timestep varaibles
tab_protein	: intance of mod_array_protein

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init_time()

subroutine init_time	(	type ( parameter_timestep ), intent(in)	param_timestep,
		type ( geometry ), intent(in)	geom,
		real ( kind=4 ), intent(in)	dist,
		real ( kind=4 ), intent(in)	rhit,
		real ( kind=8 ), intent(in)	dm30,
		real ( kind=8 ), intent(out)	dtnow,
		logical, intent(out)	hit
	)

Define instantaneous timestep if it is variable ( only for sda_2proteins )
.

Depends on position and geometry
Reduce time step near outer boundary
Small difference with sda 6 implementation (value of dthet)

Todo:

full check of dthet modifications with sda6

Parameters

param_timestep	: structure of timestep parameters
geom	: instance of geometry
dist	: distance between solutes
rhit	: distance where overlap is possible
dm30	: diff. coeff. * 30
dtnow	: return timestep
hit	: return if overlap is possible at this distance