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.
subroutine	convert_to_record_format (array_energy, array_energy_1d, max_bit_energy)
	Make format compatible to call add_record. .

Detailed Description

Version: {version 7.2.3 (2019)}

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.

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, A.Muñiz-Chicharro, R.Beccaria 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

Version: {version 7.2.3 (2019)}

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.

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 )

private

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.

Here is the caller graph for this function:

◆ 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 param_analytic : structure \ref com_sda::parameter_analytic parameter_analytic" @param param_metaldesolv : instance of \ref com_sda::parameter_metaldesolv "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

Here is the call graph for this function:

Here is the caller graph for this function:

Functions/Subroutines

Detailed Description

Function/Subroutine Documentation

◆ convert_to_record_format()

◆ mainloop_sda_2proteins_omp()