PBC : Periodic Boundary Conditions

Periodic Boundary Conditions which apply in SDA ( defined in mod_geometry.f90 )

Periodic Boundary Conditions which apply in SDA ( defined in mod_geometry.f90 )

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

---

Rules used in update_translation_box()

With a sphere geometry, no PBC is defined and a surface does not influence the algorithm
Only used for sda_2proteins, the solute starts at the b surface and the trajectory stops at the c surface
With a box geometry :

• no PBC :
  Reflexive boundary conditions along x and y. Nothing is applied along z. Should use escape ??
  Used with sda_2proteins and association rates calculation with a surface. The solute cannot go below zmin ( exclusion with the surface )
  It will escape at zmax. The procedure is an approximation, not yet validated
  
• with PBC :
  
  1. no surface : PBC in 3D, more usual case with sdamm
  2. with a surface : Keep periodic boundary conditions alonz x and y and reflexive on z.
     Due to the repulsive lennard-jones the solute should not go below the surface