MainLoop_sdamm.f90 File Reference

Functions/Subroutines
subroutine	mainloop_sdamm (tab_protein, rcriteria, o_complexes, trajectories, geom, resid_time, type_calc, param_timestep, param_force_energy, param_analytic, param_metaldesolv, timemax, old_rotation, nrun, p_restart)
	Main function for sdamm.
subroutine	compute_rdf (resid_time, tab_protein, geom)
	Call during the simulation to compute the radial distribution function.

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

---

Loop in the case of multiple proteins

Function/Subroutine Documentation

compute_rdf()

subroutine mainloop_sdamm::compute_rdf ( type ( residence_time )  resid_time, type ( array_protein_type ), intent(in)  tab_protein, type ( geometry )  geom  )

private

Call during the simulation to compute the radial distribution function.

Certainly not optimal

Parameters

resid_time	: instance residence_time
tab_protein	: instance of array_protein_type
geom	: instance of geometry

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mainloop_sdamm()

subroutine mainloop_sdamm	(		tab_protein,
			rcriteria,
			o_complexes,
			trajectories,
			geom,
			resid_time,
			type_calc,
			param_timestep,
			param_force_energy,
			param_analytic,
			param_metaldesolv,
			timemax,
			old_rotation,
			nrun,
			p_restart
	)

Main function for sdamm.

In SDAMM ( SDA with Multiple Molecules ) we simulate crowding effects
Many proteins are inside a box ( with or without PBC (periodic boundary conditions ) and are simulated for a definite time
The main output is a trajectory file

The case where a solute is a surface is treated slightly differently ( use 2 cutoffs, modify PBC )
Some, or all solutes may also be flexible

Only parts of the computation is parrallelised :

• Force computation
• Energy computation
• Brownian Dynamics move
• Radial Distribution Function ( RDF ) in compute_rdf() ( to check efficient )

Parameters

tab_protein	: instance of array_protein_type
rcriteria	: reaction criteria
o_complexes	: instance of record for complex output
trajectories	: instance of record for trajectory output
geom	: instance of geometry
resid_time	: instance of residence_time, here used for radial distribution function
type_calc	: instance of type_calculation
param_timestep	: instance of parameter_timestep
param_force_energy	: structure type_force_energy
param_analytic	: instance of parameter_analytic
param_metaldesolv	: instance of parameter_metaldesolv
timemax	: length of the trajectory

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