in.deform.polychain.txt

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#                                                   #
#                                                   #
# Filename: in.deform.polychain.txt                 #
# Author: Mark Tschopp, 2010                        #
#                                                   #
# The methodology outlined here follows that from   #
# Hossain, Tschopp, et al. 2010, Polymer.  Please   #
# cite accordingly. The following script requires   #
# a LAMMPS data file containing the coordinates and #
# appropriate bond/angle/dihedral lists for each    #
# united atom.                                      #
#                                                   #
# Execute the script through:                       #
# lmp_exe < in.deform.polychain.txt                 #
#                                                   #
#####################################################

# VARIABLES
variable fname index PE_cl100.txt
variable simname index PE_cl100

# Initialization
units		real
boundary	p p p #f f f
atom_style	molecular
log 		log.${simname}.txt
read_data	${fname}

# Dreiding potential information
neighbor	1.0 bin #0.4 bin
neigh_modify	every 1 delay 1 one 10000 # Added delay so it doesn't wait 10 steps.
bond_style      harmonic
bond_coeff	1 350 1.53
angle_style     harmonic
angle_coeff	1 60 109.5
dihedral_style	multi/harmonic
dihedral_coeff	1 1.73 -4.49 0.776 6.99 0.0
pair_style	lj/cut 10.5
pair_coeff	1 1 0.112 4.01 10.5



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# Equilibration (NVT dynamics at constant temperature)

variable myTemp equal 100.0 # Added so the temperature could be adjusted with a single change to the script
variable timeStep equal 2 # femptoseconds - Added so variables declarations can be grouped
variable outputFreq equal round(2500/${timeStep})
variable numOutputSteps equal 1000 # Number of frames in trajectory output
variable numSimSteps equal 25000000 #${numOutputSteps}*${outputFreq} # Number of timesteps the simulation will run


velocity 	all create ${myTemp} 1231 # velocity groupID style[create] temp randomSeed
timestep	${timeStep} #Set simulation timestemp
thermo_style	custom step temp #Configure thermodynamic info output style
thermo          100000 #Interval(in timesteps) on which thermodynamic data is printed

fix		1 all nvt temp ${myTemp} ${myTemp} 10.0
fix		2 all plumed plumedfile plumed.dat outfile p.log

dump 		1 all custom ${outputFreq} dump.lammpstrj id type xu yu zu #added, output every 25000 to match time of toymodel with timestep=1

run		${numSimSteps}

unfix 1
unfix 2

write_restart 	restart.${simname}.dreiding1

print "All done"