# When using LAMMPS-GUI in your project, please cite: https://arxiv.org/abs/2503.14020

#Set Up
units real
dimension 3
atom_style full
boundary p p p

#Model Definition
pair_style lj/cut 9.5 #table
bond_style harmonic #table...
angle_style harmonic #
dihedral_style opls #
improper_style cvff #

#important term for molecules to turn off double counted bond/etc.
special_bonds lj 0.0 0.0 0.5 angle yes dihedral yes

#import data file
read_data PLA600EM.lmp

#to find polymer length
group type1 type 1
group type30 type 30
group ends union type1 type30

#typical minimize
minimize 1.0e-6 1.0e-6 10000 100000

#set up outputs
thermo 2000
thermo_style custom step temp pe ke etotal
dump pla all atom 10000 dump6.lammpstrj
dump len ends custom 1000 dump6.len.txt x y z #not length but length can be calculated

#give initial temperature under NVE Ensemble
velocity all create 450.0 44863 mom yes dist gaussian
fix mynve all nve
#fix 1 all temp/csld 400.0 400.0 10.0 123321
#fix mylgv all langevin 400.0 400.0 0.1 10917

#Run
timestep 0.01
run 50000000