# LAMMPS Input File
# Licensed under CC BY 4.0
# A Set of Tutorials for the LAMMPS Simulation Package (LiveCoMS, 2025)
# By Simon Gravelle, Cecilia M. S. Alvares, Jacob R. Gissinger, and Axel Kohlmeyer
# Please cite doi.org/10.33011/livecoms.6.1.3037
# Find more on GitHub: https://github.com/lammpstutorials

kspace_style pppm 1e-5
read_restart water.restart

molecule pegmol peg.mol
create_atoms 0 single 0 0 0 mol pegmol 454756

group PEG type C CPos H HC OAlc OE

delete_atoms overlap 2.0 H2O PEG mol yes

dump viz all image 250 myimage-*.ppm type &
 type shiny 0.1 box no 0.01 &
 view 0 90 zoom 3 fsaa yes bond atom 0.8 size 1000 500
dump_modify viz backcolor white &
 acolor OW red acolor HW white &
 acolor OE darkred acolor OAlc darkred &
 acolor C gray acolor CPos gray &
 acolor H white acolor HC white &
 adiam OW 0.2 adiam HW 0.2 &
 adiam C 2.8 adiam CPos 2.8 adiam OAlc 2.6 &
 adiam H 1.4 adiam HC 1.4 adiam OE 2.6

fix mynpt all npt temp 300 300 100 x 1 1 1000
fix myrct PEG recenter 0 0 0 shift all
timestep 1.0

thermo 500
run 10000

write_restart merge.restart
# write_data merge.data # uncomment to write a .data file as well