This is a LAMMPS simulation for simulating PEG-PHEMA organogel with Lithium Chlorides performed by Yu-Cheng Lai.
The goal of this simualtion is to understand the effect of Lithium Chloride ions on the mechanical properties of PEG-PHEMA organogel.
The input data file is not provided, but is able to create through PACKMOL:
https://github.com/m3g/packmol
Other softwares for creating initial model is also recomended:
Winmostar: https://winmostar.com/en/
Material Studio: https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-materials-studio/
The total process is divided into 3 parts:
(1) Minimization:
lmp_serial -in 0_Minimize.in
(2) Equilibrium under NPT and NVT:
lmp_serial -in 1_Equilibrium.in
(3) Tensile test using NVT deform:
lmp_serial -in 2_Tensile.in
The analyzing software for the result of simualtion is performed mainly in Visual Molecular Dynamics:
https://github.com/nbcrrolls/vmd
TCL script used for analyzing is provided:
(1) End-to-end distance and radius of gyration of per PEG and PHEMA polymers:
vmd -dispdev text -e 0_EL_Rg.tcl
(2) Hydrogen bond calculation due to different group of polymers (PEG-PEG / PEG-PHEMA etc...)
vmd -dispdev text -e 1_Hydrogen_bond.tcl
Hydrogen bond with self definition is also provided in 1_Hydrogen_bond_self_define.tcl with the distance between hydrogen and acceptor < 3.5 angstrom and angle > 150 degree
vmd -dispdev text -e 1_Hydrogen_bond_self_define.tcl
(3) Coordination bond calculation
vmd -dispdev text -e 2_Coordination_Bond.tcl
(4) Ion cluster search
vmd -dispdev text -e 3_Ion_cluster.tcl