# LAMMPS Description for system of 144bp-dsDNA modeled as bead-spring chain.

units	real
atom_style	full

# Declare variables.
variable	T equal 298.150000 # Simulation temperature [Kelvin].
variable	Myd equal 75.547862 # Dielectric constant of water (Depends on T and SaltCon.).
variable	Kappa equal 0.129777 # Inverse of the Debye length [A^-1].

# Random number seed for Langevin integrator.
variable	Random equal 12345

# Specify the different interaction styles.

# Bond style.
bond_style	harmonic/omp
special_bonds	lj/coul 1.0 1.0 1.0

# Angle style.
angle_style	harmonic/omp

# Dielectric constant.
dielectric	${Myd} # Dielectric constant of water (Depends on T and SaltCon.).

# Pair styles.
pair_style	lj/cut/coul/debye/omp ${Kappa} 35.5 560.600000

# Boundary conditions.
boundary	f f f

# Turn on Newton's 2nd law.
newton	on

# Read in the configuration data file.
read_data	144bp-dsdna.conf

# Bond coeff..
bond_coeff	1 50.000 20.591

# Angle coeff..
angle_coeff	1 11.000 180.000

# Pair coeffs..
# Pair coeff	types-of-atoms eps. sig.
pair_coeff	* * 0.900 16.000

# Pair modify.
pair_modify	shift yes

# Specify parameters for the neighbor list.
neighbor	3.0 bin
neigh_modify	every 1 delay 0 check yes

# Initialize velocities.
velocity	all create ${T} ${Random}

# Specifying a Langevin integrator to perform a simulation in the NVT ensemble.
fix	1 all langevin ${T} ${T} 482.550466 ${Random} gjf yes zero yes
fix	2 all nve

# Specifying the frequency of thermodynamic output.
thermo	1000
thermo_style	multi

# Write the new configurations to file.
dump	1 all molfile 1000 traj.xyz xyz /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
dump_modify	1 element dsDNA

# Minimization.
minimize	1.0e-7 1.0e-9 1000 10000

# Re-Pair modify.
pair_modify	shift no

# A timestep of 0.3 ps.
timestep	300.0

# Run X number of steps
run	100000

# Pair modify.
pair_modify	shift yes

# Minimization.
minimize	1.0e-7 1.0e-9 1000 10000

# New fix
fix	3 all ave/time 1 1 17000000 c_thermo_temp file Temp.txt

# Re-Pair modify.
pair_modify	shift no

# New dump file (after equilibrium).
dump	2 all molfile 1000 ftraj.xyz xyz /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
dump_modify	2 element dsDNA

# Re-Run X number of steps
run	17000000