conformationalisomerismlab

Revisiting the conformational isomerism of di-haloethanes; a hybrid computational and experimental laboratory for the undergraduate curriculum

https://github.com/praiteri/conformationalisomerismlab

Repository

Revisiting the conformational isomerism of di-haloethanes; a hybrid computational and experimental laboratory for the undergraduate curriculum

README

This repository contains the input files for the computational work described in:
"Revisiting the conformational isomerism of di-haloethanes; a hybrid computational and experimental laboratory for the undergraduate curriculum"
published in ACS Physical Chemistry AU 

SOFTWARE REQUIREMENTS
All the QM calculations have been performed with ORCA 5.0.2
All the MD simulations have been performed with LAMMPS and the input files were tested 
with the "release" version downloaded from github on 23rd November 2022.
LAMMPS must be compiled with these extra packages:
  * KSPACE
  * MOLECULE
  * EXTRA-FIX
  * EXTRA-DUMP
  * EXTRA-MOLECULE

PROVIDED FILES
The folder "docs" contains the instructions to the students, which include
  * Introduction to the problem
  * Short introduction to the computational methods
  * Detailed instructions for running the calculations on a LINUX VM
  * Instructions to run the experiments using the micro-RAMAN scanning probe
  * Details about the assessment

The folder "geometries" contains the atomic coordinates for the DFT and Molecualr Dynamics calculations
  * ORCA
    + DBE relaxed geometries of the anti conformer -> dbe_anti.xyz
    + DBE relaxed geometries of the gauche conformer -> dbe_gauche.xyz
    + DBE relaxed geometries of the transition state -> dbe_ts.xyz
    + DCE relaxed geometries of the anti conformer -> dce_anti.xyz
    + DCE relaxed geometries of the gauche conformer -> dce_gauche.xyz
    + DCE relaxed geometries of the transition state -> dce_ts.xyz
  * LAMMPS
    + DBE - coordinates of liquid in PDB format -> dbe_liquid.pdb
    + DBE - coordinates of liquid in LAMMPS format -> dbe_liquid.lmp
    + DBE - coordinates of isolated molecule in PDB format -> dbe_gas.pdb
    + DBE - coordinates of isolated molecule in LAMMPS format -> dbe_gas.lmp
    + DCE - coordinates of liquid in PDB format -> dce_liquid.pdb
    + DCE - coordinates of liquid in LAMMPS format -> dce_liquid.lmp
    + DCE - coordinates of isolated molecule in PDB format -> dce_gas.pdb
    + DCE - coordinates of isolated molecule in LAMMPS format -> dce_gas.lmp

The folder "inputFiles" contains the input files for ORCA and LAMMPS
  * ORCA input file for the geometry optimisation and frequency calculation -> orca.geopt.inp
  * ORCA input file for the Nudged Elastic Band calculation (transition state) -> orca.neb.inp
  * LAMMPS input file that contains the instructions for the MD calculations -> lammps.inp
  * Forcefield file for the DCE/DBE interactions in LAMMPS format -> forcefield.lmp

The folder "MDAnalysis" contain
  * python script to compute the distribution of the torsional angle 
    - the following python packages are required: MDAnalysis, matplotlib and numpy
  * example of input and output files

Owner

Citation (CITATION.cff)

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Paolo
    given-names: Raiteri
    orcid: https://orcid.org/0000-0003-0692-0505
title: praiteri/conformationalIsomerismLab: First release
version: v1.0
date-released: 2022-12-20

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