# 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 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

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 dphi PEG dihedral/local phi

thermo_style custom step temp etotal c_rgyr

thermo 250

dump mydmp all local 50 pull.dat index c_dphi

run 15000

fix myaf1 topull1 addforce 10 0 0

fix myaf2 topull2 addforce -10 0 0

run 15000