CIDMD_analysis

Authors: Jesi Lee

General Description

• These scripts analyze CIDMD (collision-indueced dissociation molecular dynamics) simulations in TeraChem.

Organization

For the scripts to work properly,

• Molecule/mol_info.in is required (for details, see CIDMD_setup/README.md in the repository github.com/jesilee/CIDMD_setup.
• The CIDMD trajectories should have been processed with LearnReactions.py, and this repository should be located at Molecule/cid/CIDMD_analysis and
• Each resulting subfolder Molecule/cid/results/ will be created containing these resulting files: cidmd.jdx, cidmd.msp, cidmd.PS_case1_RCID_vfac8-cut05norm.png, cidmd.PS_case1_RCID_vfac8-cut05.png, ar_vel_KE.png,sy_found.out, total_gputime.txt, pop_found.out, rxn_found.out, report_found.out.

Inputs

• learn_rxn.log files located in Molecule/cid/calcs/XXX/gathered/ that resulted from post-processing CIDMD by running LearnReactions.py written by Prof. Lee-Ping Wang. His repository: 'https://github.com/leeping/nanoreactor' (not yet released)
• mol_info.in file located in Molecule/

Outputs

• results folder under Molecule/cid/ containing these files: cidmd.jdx, cidmd.msp, cidmd.PS_case1_RCID_vfac8-cut05norm.png, cidmd.PS_case1_RCID_vfac8-cut05.png, ar_vel_KE.png,sy_found.out, total_gputime.txt, pop_found.out, rxn_found.out, report_found.out.

• cidmd.jdx, cidmd.msp: CIDMD theoretical mass spectrum in JDX and MSP file format. Both file format are useful for the NIST programs or other mass spectra libraries.

• cidmd.PS_case1_RCID_vfac8-cut05norm.png, cidmd.PS_case1_RCID_vfac8-cut05.png: PNG format pictures of normalized and not normalized CIDMD theoretical mass spectra.

• ar_vel_KE.png: a PNG format picture of argon velocities as a function of collision time (usually less than 1 picosecond).

• sy_found.out : a survival yield value for molecular ion during CIDMD trajectories.

• total_gputime.txt : total gpu compute time for CIDMD in seconds and hours.

• pop_found.out : calculated charges of each fragments during CIDMD trajectories

• rxn_found.out : detected reactions by LearnReactions.py during CIDMD trajectories

• report_found.out : a summary of fragments and thier charges during CIDMD trajectories.

Dependencies

• python 3.6
• numpy
• pandas
• matplotlib
• these files from this repo should be in the current working directory: CIDMD_analysis.com CIDMD_analysis.py
• LearnReactions.py written by Prof. Lee-Ping Wang. His repository: 'https://github.com/leeping/nanoreactor' (not yet released)
• Molecule/cid/calcs/XXX/gathered/learn_rxn.log (this would be the resulting output file from running LearnReactions.py)
• Molecule/mol_info.in (please see 'https://github.com/jesilee/CIDMD_setup/blob/main/README.md' for an example)

Important notes

To start CIDMD, Folder organization is very important. Please see the instruction to set up CIDMD here: 'https://github.com/jesilee/CIDMD_setup/blob/main/README.md'