Network Extraction¶

In this second step of the workflow a reaction network is extracted, and the individual molecules are optimized.

Initial Network from ChemTrayzer2¶

To extract the reaction network, ChemTraYzer2 is used. By default, only the trajectories from simulations that terminated normally are used for network extraction. The reaction network is fully stored in the ams.rkf file, as well is in the file reaction_network.gml, which can be directly read into the networkx python module. Reaction network information is also printed to output, and the details of the latter can be set in the input block NetworkExtraction%Print. In the output, the molecules are listed in order of their net flux; The difference between the number of instances at the end of the simulation and the number of instances at the start of the simulations. At this first approximation, products with the highest positive net flux are considered to be the most stable.

Geometry Optimization¶

For all unique molecules, an attempt is made to find the optimized geometry for that molecule. For each molecule the coordinates are extracted either from the molecular dynamics runs (reported with source file, frame and atom ids) or constructed from the SMILES string using from_smiles. Finally, a geometry optimization is performed and each molecule is assigned the total energy corresponding to the optimized geometry. If the geometry optimization fails, or if our bond guessing algorithm predicts a different connectivity after optimization, the energy of the unoptimized coordinates is used instead. If desired, the geometry optimizations can be performed with a different engine, e.g. using an implicit solvent, if this better approximates the target experimental reaction conditions. To do this, first perform a run with molecular dynamics only and then perform a restart with molecular dynamics disabled and the engine of choice defined in the input.

Molecular Charge Assignment¶

In order to correctly perform geometry optimizations, the charge of each molecule needs to be determined beforehand. The charges are obtained by collecting the atomic charges from the output of the molecular dynamics simulations, averaging the resulting molecular charges over the relevant frames, and rounding to integer values. Every molecule will be connected to at most 2 reactions; The reaction that creates it, and the reaction that destroys it. A check is performed, to see if all the reaction charges are balanced. If this is not the case, then the corresponding molecular charges are adjusted to ensure charge balance through-out. The charge adjustments are restricted in that the change \(\Delta q\) per molecule may not exceed 1.0e. If unbalanced reactions still remain after the charge adjustments, then an ionization reaction is added, connecting two versions of the molecule, each with a different charge.

Manual specification of MD trajectories¶

You can run the network extraction on any MD trajectories, even if they were not calculated by the Reactions Discovery tool.

If

MolecularDynamics%Enabled is True, then those MD trajectories will be used for the network extraction,
MolecularDynamics%Enabled is False, then you can specify a directory with ams.rkf files to analyze with NetworkExtraction%MDTrajectories

Example:

MolecularDynamics Enabled=No
NetworkExtraction Enabled=Yes MDTrajectories=/some/path

Unfinished simulations are only used if NetworkExtraction%ExtractFromFailedMDJobs is enabled.

NetworkExtraction
   Enabled Yes/No
   ExtractFromFailedMDJobs Yes/No
   MDTrajectories string
   Print
      FilterFluctuations Yes/No
      MaxReactionOrder integer
      MinReactionsThreshold integer
      SkipRareReactions Yes/No
   End
   UseCharges Yes/No
End

NetworkExtraction

Type: Block
Description: Options for extracting the reactive network from MD trajectories

Enabled

Type: Bool
Default value: Yes
GUI name: NetworkExtraction
Description: Whether to perform network extraction.

ExtractFromFailedMDJobs

Type: Bool
Default value: No
GUI name: Extract from failed MD jobs
Description: Whether to extract from failed/crashed MD jobs (by default, only successful jobs are used)

MDTrajectories

Type: String
GUI name: MD Trajectories
Description: If MolecularDynamics%Enabled is False, this directory will be recursively scanned for ams.rkf files containing MD trajectories. All found trajectories will be used for the analysis. It should typically be a Reactions Discovery results directory containing finished MD simulations.

Print

Type: Block
Description: Printing details

FilterFluctuations

Type: Bool
Default value: Yes
Description: If true, do not print molecules that are only part of recrossing reactions.

MaxReactionOrder

Type: Integer
Default value: 4
Description: If the reaction order is larger than this value, the reaction will not be printed.

MinReactionsThreshold

Type: Integer
Default value: 3
Description: If a molecule is involved in fewer reaction than this value, skip printing the results corresponding to it. To print all molecules, set this value to 0.

SkipRareReactions

Type: Bool
Default value: Yes
Description: If true,reduce the output by filtering out rare reactions. If false, always print all reactions.

UseCharges

Type: Bool
Default value: Yes
Description: Use engine-calculated charges if they exist on the MD trajectory files for the NetworkExtraction