SDA (SDA flex)  7.2
Simulation of Diffusional Association
PBC : Periodic Boundary Conditions

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

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

Version
{version 7.2.3 (2019)}

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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 :

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