MainLoop_sda_2proteins_omp.f90 File Reference

Data Types
interface	change_conformation
	called if flexible More...

Functions/Subroutines
subroutine	mainloop_sda_2proteins_omp (tab_protein_unique, rcriteria, o_complexes, trajectories, geom, p_restart, resid_time, type_calc, param_timestep, param_probe, param_force_energy, param_analytic, param_metaldesolv, option_omp, nmax_overlap, rboost, timemax, nrun, old_rotation)
	MainLoop_sda_2proteins_omp. More...
subroutine	convert_to_record_format (array_energy, array_energy_1d, max_bit_energy)
	Make format compatible to call add_record. . 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

---

Parralel version of sda 2proteins with OpenMP

Main loop for BD with 2 solutes
Used for normal sda or sda_koff
Can compute association rate, docking or electron transfert calculation with 2 proteins,
Residence time, first passage time

Function/Subroutine Documentation

convert_to_record_format()

subroutine mainloop_sda_2proteins_omp::convert_to_record_format	(	real(kind=8), dimension(:,:), intent(in)	array_energy,
		real(kind=8), dimension(:,:), intent(out)	array_energy_1d,
		integer, intent(in)	max_bit_energy
	)

Make format compatible to call add_record.
.

could be in record, and get bit information from there. need a parameter, maximum max_bit_energy to limit the loop of the array.

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mainloop_sda_2proteins_omp()

subroutine mainloop_sda_2proteins_omp	(		tab_protein_unique,
			rcriteria,
			o_complexes,
			trajectories,
			geom,
			p_restart,
			resid_time,
			type_calc,
			param_timestep,
			param_probe,
			param_force_energy,
			param_analytic,
			param_metaldesolv,
			option_omp,
			nmax_overlap,
			rboost,
			timemax,
			nrun,
			old_rotation
	)

MainLoop_sda_2proteins_omp.

Main function for 2 solutes computation

Parameters

tab_protein_unique	: contains all proteins, instance of array_protein_type
rcriteria	: instance of react_criter
o_complexes	: for writing complexes
trajectories	: for writing trajectory
geom	: geometry instance
p_restart	: pointer on a restart record
resid_time	: instance of residence_time
type_calc	: instance of type_calculation
param_timestep	: instance of parameter_timestep
param_probe	: instance of probe_type
param_force_energy	: instance of type_force_energy
param_analytic	: structure parameter_analytic
param_metaldesolv	: instance of parameter_metaldesolv
option_omp	: option for openmp
nmax_overlap	: could with other parameter
rboost	: distance of boost
timemax	: maximum time for a trajectory, 0 means infinite
nrun	: number of runs
old_rotation	states whether the old rotation should be used or the one via Rodrigues formula

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