SDA  7.1
Simulation of Diffusional Association
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MainLoop_sdamm.f90 File Reference

Loop in the case of multiple proteins. More...

Data Types

interface  change_conformation
 called if flexible More...
 

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)
 Main function for sdamm. More...
 
subroutine compute_rdf (resid_time, tab_protein, geom)
 Call during the simulation to compute the radial distribution function. More...
 

Detailed Description

Loop in the case of multiple proteins.

Version
{version 7.1 (2015)}

Copyright (c) 2009, 2010, 2015 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) formerly EML Research gGmbH (EML-R ) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Copyright (c) 2000, 2003 European Molecular Biology Laboratory Meyerhofstr. 1, Postfach 10.2209 D-69012, 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/doc/doc_sda7/references.html):

Brownian dynamics simulation of protein-protein diffusional encounter.

(1998) Methods, 14, 329-341.

Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, R.R.Gabdoulline, M. Ozboyaci, S.Richter and R.C.Wade


Function/Subroutine Documentation

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

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

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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