Hi Axel,

Yes I know that MSD =! RMSD. Still the slope from MSD does not give me a value that makes sense.

Yes I know that system is argon. But I want to calculate diffusion coefficient after the effect of using ATC so i wanted to see if the process works

Yes I visualized the system. No Its not liquid yes but the atoms are moving. It should be liquid above 1700 K

I have attached my file here.

#Making Melt Fe3c Modeled after in.elastic and Melt File made by Carlos Ruestes

units metal

atom_style full

boundary p p p

neighbor 0.3 bin

neigh_modify every 20 delay 0 check no

read_data data.Fe3C.xtal.3x3x3

change_box all triclinic

pair_style meam/c

pair_coeff * * Fe3C_library_Liyanage_2014.meam Fe C Fe3C_Liyanage_2014.meam Fe C

# Define minimization parameters

variable etol equal 1.0e-3

variable ftol equal 1.0e-10

variable maxiter equal 100

variable maxeval equal 1000

variable dmax equal 1.0e-2

# Define MD parameters

variable nevery equal 10 # sampling interval

variable nrepeat equal 10 # number of samples

variable nfreq equal {nevery}*{nrepeat} # length of one average

variable nthermo equal {nfreq} # interval for thermo output
variable nequil equal 10*{nthermo} # length of equilibration run

variable nrun equal 3*${nthermo} # length of equilibrated run

variable inittemp equal 1200.0 # temperature of initial sample

variable hightemp equal 1200.0 # temperature of above melting sample

variable timestep equal 0.001 # timestep

variable mass1 equal 28.06 # mass

variable adiabatic equal 0 # adiabatic (1) or isothermal (2)

variable tdamp equal 0.01 # time constant for thermostat

variable seed equal 123457 # seed for thermostat

variable tdamp equal “v_timestep*10" # May require some systematic tests for proper adjustment*

variable pdamp equal "v_timestep100” # May require some systematic tests for proper adjustment

# Setup minimization style

min_style cg

min_modify dmax ${dmax} line quadratic

thermo 100

thermo_style custom step temp vol press ke pe etotal

# Compute initial state

fix 3 all box/relax aniso 0.0

minimize {etol} {ftol} {maxiter} {maxeval}

velocity all create {inittemp} {seed} rot yes dist gaussian

dump id all atom 500 dump.melt5

reset_timestep 0

fix equilibration all npt temp {inittemp} {hightemp} {tdamp} iso 0 0 {pdamp}

run 2000000

#fix equilibration all npt temp {hightemp} {inittemp} {tdamp} iso 0 0 {pdamp}

#run 20000

#fix equilibration all npt temp {inittemp} {inittemp} {tdamp} iso 0 0 {pdamp}

#run 20000

write_data data.meltFe3C.* # data file for restarts

print “all DONE”

write_restart meltFe3c.r