mod_crowder.f90 File Reference

Data Types
type	mod_crowder::crowder
	Type to define a crowder. More...

Modules
module	mod_crowder

Functions/Subroutines
subroutine	mod_crowder::new_sphere_crowder (this, dh_rad, rep_rad, array_dh_rad, array_rep_rad, ionic, rep_bfct, h_size, max_dist)
	Constructor for crowder type.
subroutine	mod_crowder::delete_crowder (this)
	Destructor for crowder type.

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

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Contains routines relating to CG crowder interaction

Module for defining and creating crowder interactions.
At present crowders are purely speherical and defined by two types of interaction:

• A Debye-Hueckel sphere electrostatic model
  • Two parameters for each solute define this: formal charge and radius
• A soft-core repulsive term with a hard core, as defined in Tokuyama Phys Rev E 2011
  • Tokuyama used particles same diameter, but repulsion term easily transferable to different spheres using sum of radii.

More terms could be added by expanding the crowder type.

Shape option present to allow grid-like interactions using simplified models. – Not implemented

These interactions are described using precomputed 1D arrays for force and energy, as in long range DH correction.

NOTE: - At present if a flexible solute is set to being a crowder, the same crowder parameters are used for all flexible representations.

• As crowders objects are members of the mod_setofgrid::sogrid class, this can easily be changed by assigning different crowders to each sogrid of the mod_flexibility::flexible class of the flexible mod_protein::protein object.
  • Would require that radii, and possibly charges, are moved to conformation dependent part of input file.
  • Also would need to ensure interacting solutes use correct 1D array values for relevent conformation.