read_input_file.f90 File Reference

Functions/Subroutines
subroutine	read_input_file (tab_protein, rcriteria, resid_time, o_complexes, trajectories, geom, p_restart, type_calc, param_timestep, param_probe, param_force_energy, param_analytic, param_metaldesolv, param_pmf, option_omp, timemax, rboost, nrun, nmax_overlap, account_occurency)
	Function to read the input file and allocate all proteins, grids, flexible and all other variables. More...
subroutine	read_list_conf (plist_flex, input_param, counter_grid, filename, param_probe, param_analytic, tmp_exclud, center, rcriteria, type_calc, been_read, fixed_cent)
	Read a list of conformations for flexible solutes. More...
subroutine	initialize_bits (o_record, tab_prot)
	Initialize bits. More...
subroutine	initialize_movable_atoms (type_calc, tab_prot)
	Initialize arrays for movable atoms. More...
subroutine	initialize_random_generator (type_calc, dseed)
	Initialize the random number generators. 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

---

Main function to read sda input file

Function/Subroutine Documentation

initialize_bits()

subroutine initialize_bits	(	type ( record )	o_record,
		type ( array_protein_type ), target	tab_prot
	)

Initialize bits.

Could be in mod_record array_prot is included now.

Could use param_force_energy, but bits info needed for creating array for trajectory to check if possible to setup param_force_energy before any record is initialized

Initialize bits, depending on the loaded grids ( bit_energy ) and type type calculation ( bit_integer )

Parameters

o_record	: instance of mod_record::record
tab_prot	: instance of array_protein_type

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initialize_movable_atoms()

subroutine initialize_movable_atoms	(	type ( type_calculation )	type_calc,
		type ( array_protein_type )	tab_prot
	)

Initialize arrays for movable atoms.

Initialize the pointers of array of movable atoms for proteins
Check if they can be common and allocated into mod_setofgrid::sogrid, or if a local copy is needed into each protein
By default, points to sogrid. If needed, make a local copy for each protein (sdamm, sda_flex protein 2). If possible delete the copy in sogrid ( sdamm )
Do not account for OpenMP here, will be done in copy_array_protein

Parameters

type_calc	: instance of mod_type_calc::type_calculation "type_calculation"
tab_prot	: instance of array_protein_type

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initialize_random_generator()

subroutine initialize_random_generator	(	type ( type_calculation )	type_calc,
		real ( kind=8 )	dseed
	)

Initialize the random number generators.

If dseed is equal to zero, the time is used as a seed, otherwise use the provided dseed

Initialze both generator ( see RNG : Random Number Generator ):

• without OpenMP : only one seed is used
• with OpenMP : each thread N uses the seed dseed+N

Parameters

type_calc	: instance of type_calculation
dseed	: input seed for RNG, if 0 use the time

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read_input_file()

subroutine read_input_file	(	type ( array_protein_type )	tab_protein,
		type ( react_criter ), target	rcriteria,
		type ( residence_time )	resid_time,
		type ( record )	o_complexes,
		type ( record )	trajectories,
		type ( geometry )	geom,
		type ( record ), pointer	p_restart,
		type ( type_calculation )	type_calc,
		type ( parameter_timestep )	param_timestep,
		type ( probe_type )	param_probe,
		type ( type_force_energy )	param_force_energy,
		type ( parameter_analytic )	param_analytic,
		type ( parameter_metaldesolv )	param_metaldesolv,
		type ( parameter_pmf )	param_pmf,
		type ( type_option_omp )	option_omp,
		real ( kind=8 ), intent(out)	timemax,
		real ( kind = 4 )	rboost,
		integer	nrun,
		integer	nmax_overlap,
		logical	account_occurency
	)

Function to read the input file and allocate all proteins, grids, flexible and all other variables.

Print summary informations about parameters

Simple variable read by read_single_parameter :

• number of runs, timemax, probe, scale factor for grids...

Use of groups/block for complexe modules, read by read_group :

• No maximum predefined number of Solute_Grid groups
• No maximum predefined Flexible list and proteins
• Could be extended to more than one reaction criteria ??

Inconvenient:

• Order of some GROUPs are important

Parameters

tab_protein	: instance of array_protein_type
rcriteria	: instance of react_criter
resid_time	: instance of residence_time
o_complexes,trajectories,p_restart	: instance of record
geom	: instance of geometry
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	: definition of analytical interaction, instance of parameter_analytic
param_metaldesolv	: instance of parameter_metaldesolv
option_omp	: used for OpenMP
timemax	: maximum time for each trajectory, 0 is infinite
rboost	: distance when boost
nrun	: number of trajectories
nmax_overlap	: number of overlap before applying a boost
account_occurency	: if occurences must be accounted

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read_list_conf()

subroutine read_list_conf	(	type ( list_flex_type )	plist_flex,
		type ( param_list )	input_param,
		integer	counter_grid,
		character ( 128 )	filename,
		type ( probe_type )	param_probe,
		type ( parameter_analytic )	param_analytic,
		logical	tmp_exclud,
		real ( kind=8 ), dimension(3)	center,
		type ( react_criter )	rcriteria,
		type ( type_calculation )	type_calc,
		logical	been_read,
		real ( kind=8 ), dimension( 3 ), intent(in)	fixed_cent
	)

Read a list of conformations for flexible solutes.

Read an external input file
Two methods implemented :

• EXPLICIT : give the names of all grids explicitely
• IMPLICIT : use an automatic numerotation ( eg : pbd1.pdb, pdb2.pdb,... ), need additional parameters

If not flexible return the correct name of the grid ( used if fparrallel )

Parameters

plist_flex	: instance of list_flex_type
input_param	: instance of param_list
counter_grid	: use as identifier for grids
filename	: name of external file with the list of conformations
param_probe	: instance of probe_type
param_analytic	: structure parameter_analytic
tmp_exclud	: if exclusion must be computed
center	: center of solutes ?
rcriteria	: instance of react_criter
type_calc	: instance of type_calculation
been_read	: used for checking misspelling

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