User defined output files of SDA7
standard output(*.ou)
The standard output contains a description of the Brownian dynamics run and results
If OpenMP is activated, the following information is printed by each thread:
  • Parameters of simulations read from the input file(s).
  • Mean residence times are computed and printed (after the simulations are finished) in every 1 Å slab of inter-solute center-to-center separation.
  • The main results of simulations - generally the association rate constants - are printed for every distance window and every number of contact pairs.
  • The execution time of the program is printed for initialization and simulation parts.
  • At the end of the simulations, the statistics over all runs are computed and printed out. These are:
    • number of Brownian dynamics steps during all simulations
    • the duration of the simulations in ps
    • above value scaled per run
    • number of solute overlaps (when the step is repeated) that occurred
    • number of boosts, when the solutes are artificially displaced.
fcomplexes
Complexes satisfying the reaction criteria conditions are written to this file (see file format). These complexes can be processed further for clustering or to generate pdb or dcd complexes files.
trajectories
Store trajectory for SDAMM or sda_2proteins
pdb_filename.access
if save_access is activated, computes and writes the solvent accessibility of the atoms on the surface. Then this file is read by other programs.
pdb_filename.excl.ascii/bin.grd
if save_exclusion is activated, writes the exclusion grid into a UHBD grid in ascii or binary format. It can be visualized with VMD.
resid3d.bin.grd
if type_residence = resid_3d is chosen within GROUP = ResidenceTime, it will produce a binary UHBD grid with each coordinate having the sum of the residence times of the center of geometry of the ligand at that coordinate (can be visualized e.g., in VMD)
Log files
association_rate/ electron_transfer / fpt.log
If bootstrap is activated, this file contains the data for every trajectory. It is intended to be used by the python script auxi/Bootstrap_multiCPU.py
steps.log
In case of a 2-solute simulation, print the number of trajectories generated (and their corresponding number of steps). It is regularly updated every 100 trajectories.
reaction_criteria.log .
Only if a reaction criteria input file is provided (*.rxna file). This file contains information extracted from the input file and the pdb. It can be visualized with VMD (to load as pdb).
exclusion_grids.log
In case of a 2-solute simulation, print information about the exclusion grid calculation.

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