The ChemTraYzer scripts, developed in the Leonhard group at Aachen University, provide a methodology for deducing quantitative reaction models from reactive molecular dynamics (MD) simulations by identifying, quantifying, and evaluating elementary reactions of MD trajectories.
For usage with AMS, the scripts have been slightly modified and use RDKit instead of the openbabel-bindings. The original paper, Automated Discovery of Reaction Pathways, Rate Constants, and Transition States Using Reactive Molecular Dynamics Simulations, can be found here.
Command line execution¶
1. Open a terminal:
- on Linux: Ctrl+Alt+T usually works, otherwise browse your application menus
- on Windows: double click adf_command_line.bat in your ADF installation directory (e.g. C:/ADF2016.106), enter ‘sh’ to go to a shell
2. cd into the directory where your trajectories are located with the terminal
3. Assuming your trajectory file is located in directory called
jobname.results, running ChemTraYzer is a two step procedure
- run the processing step (with default values)
$AMSBIN/amspython $AMSHOME/scripting/standalone/chemtrayzer/processing_scm.py jobname.results
- run the analysis step (with default values)
$AMSBIN/amspython $AMSHOME/scripting/standalone/chemtrayzer/analyzing_scm.py jobname.results
You will probably want to adjust the settings. A list of all available options is shown by calling the scripts without arguments, e.g.
ChemTraYzer creates several output files, the most relevant ones being:
1st line: indices of the species, e.g. S1;S2;S3;etc…
2nd line: SMILES of the species, e.g. ;C;CC;CCO;CCOO;CO;O;[H];etc…
3rd - end: timestep, counts of the species, e.g. 150;0;0;2;… // step 150, current count of S3 == 2
1st line: indices of the reactions, e.g. t [steps];R0;R0*;R1;R1*; // a “*” marks the back reaction
2nd line: the reactions formulated with the species indices, e.g. S0 + S0 + S0 + S13 -> S65; // see reac.spec.tab
3rd line: the reactions formulated with sum formulas, e.g. CH3 + H -> CH4, etc…
4th -…: timestep; rate constant of the reaction; rate constant of the back reaction; etc…
folder containing the 2D structures (if obabel was able to create them) reac.pic/xyz/ xyz files of the species as they first appeared in the trajectory