1. ABOUT THE DATASET
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Title:	Dataset for "In Silico Interactome of a Room-Temperature Ferroelectric Nematic Material"

Creator(s): Richard Mandle

Organisation(s): University of Leeds

Rights-holder(s): Copyright 2023 University of Leeds

Publication Year: 2023

Description: Contains gromacs binary runfiles (*.tpr) for executing simulations, GAFF topology for UUQU-4-N generated with the Acpype script, and analysis code used in this work.

Cite as: Richard Mandle (2023): Dataset for "In silico interactome of a room-temperature ferroelectric nematic liquid crystal"; https://doi.org/10.5518/1355

Related publication: https://doi.org/10.3390/cryst13060857

Contact: r.mandle@leeds.ac.uk


2. TERMS OF USE
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 Copyright 2023 University of Leeds, this dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/.]


3. PROJECT AND FUNDING INFORMATION
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Title: A New Order of Liquids

Dates: 01/04/2022 to 01/04/2026 

Funding organisation: UKRI

Grant no.: MR/W006391/1

4. CONTENTS
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File listing

 DIRECTORY\FILE:

 code\analysis.sh - bash script for post-simulation analysis
 code\calc_OP.job - SGE job submission script for order parameter calculation
 code\OP.py       - python script called by above SGE jobscript
 code\setup.sh    - bash script for quick simulation setup

gromacs_tpr\isotropic.tpr - gromacs binary run file for an isotropic start
gromacs_tpr\polar.tpr     - gromacs binary run file for a polar nematic start

UUQU4N-acpype\UUQU4N.gro  - optimised geometry of UUQU4N in .gro format
UUQU4N-acpype\UUQU4N.itp  - GAFF Forcefield paramters for UUQU4N, generated by acpype
UUQU4N-acpype\UUQU4N.mol2 - optimised geometry of UUQU4N with RESP chages in mol2 format
UUQU4N-acpype\UUQU4N.top  - base topology file generated by acpype


5. METHODS
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analysis scripts were written by the author.

gromacs .tpr files were generated with Gromacs/2019.2 

acpype/topology files were generated by optimising the geometry using the Gaussian G09 suite of programs and calculating RESP charges; this was converted to MOL2 format using the Antechamber tool in Amber20; the MOL2 file was then passed to the acpype script to generate the GAFF forcefield parameters.