Tutorial 4

Molecular dynamics from XYZ.

From: Thermal equilibration of Spironapthopyran (Raison Dsouza).

The following is a thermal equilibriation dataset of Spironapthopyran (SNP) molecular crystal unit cell. Spiropyrans are a class of photochromic systems which isomerize into a "cis"-form product state when irradiated with UV/Visible light and once it's removed, perform a cyclo-reversion to the initial reactant state.
The usual cycle for Spiropyrans is the conversion to Merocyanine (which is a ring-open form).
This isomerization (usually involving large structural change) gives a great platform for using Ultrafast Electron Diffraction (UED) technique [1] (spatial & time resolution).
This thermal run is an initial condition generator for the actual QM/QM [2] type dynamics simulations.

[1] Capturing Chemistry in Action with Electrons: Realization of Atomically Resolved Reaction Dynamics.
Ischenko AA, Weber PM, Miller RJD. Chem Rev. 2017 Aug 23;117(16):11066-11124

[2] Hybrid QM/QM Simulations of Excited-State Intramolecular Proton Transfer in the Molecular Crystal 7-(2-Pyridyl)-indole
Michal A. Kochman and Carole A. Morrison. J. Chem. Theory Comput., 2013, 9 (2), pp 1182–1192

Bibtex

Data Preparation

We begin with an XYZ file (the file format is described here):

trajectory.rar

and (optionally) information about the unit cell parameters:

14.613700 0.0000 0.000000
-0.00000 12.6946000 0.00000
-4.550830 -0.00000 18.954210

Overview

We create a config file to load the XYZ file which contains 800 timesteps:

dsouza.ncfg

atomscaling 0.6
displaybonds

xyzfile "trajectory.xyz"

background 0 0 0

Optionally, the unit cell parameters can be passed using the abc parameter, separated by spaces:

abc 14.613700 0.0000 0.000000         -0.00000 12.6946000 0.00000           -4.550830 -0.00000 18.954210
repetitions 1 2 1
displayunitcell

Optionally, we may pass some parameters regarding visualization and interaction in the HTC Vive viewer

showcontrollers
hapticfeedback

 

SNP

Additional parameters to control colouring

bondscolour 0.5 0.5 0.5
atomtrajectorycolour 1 1 0
supercellcolour 0 1 1
unitcellcolour 1 1 1

Display the trajectory of first atom

showtrajectory 1