# 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 merge.restart

group ends type OAlc
variable xcm equal xcm(ends,x)
variable oxies atom type==label2type(atom,OAlc)
variable end1 atom v_oxies*(x>v_xcm)
variable end2 atom v_oxies*(x<v_xcm)
group topull1 variable end1
group topull2 variable end2

dump mydmp all atom 1000 pull.lammpstrj

timestep 1.0
fix mynvt all nvt temp 300 300 100
fix myrct PEG recenter 0 0 0 shift all

compute rgyr PEG gyration
compute prop PEG property/local dtype
compute dphi PEG dihedral/local phi

thermo_style custom step temp etotal c_rgyr
thermo 250

run 15000

fix myaf1 topull1 addforce 10 0 0
fix myaf2 topull2 addforce -10 0 0

run 15000