I am supposed to determine thermal conductivity of a molecular crystal TKX 50 using green-kubo method according to lammps example file. Data file is attached but result is highly fluctuating. Could you please suggest any solution.
You can check out this discussion:
https://matsci.org/t/green-kubo/37429
Without knowing the specifics of your simulation.
You converted a script for Argon to some Molecular crystal.
I would guess it is probably a combination of short thermostat time, short equilibrium time and sampling times - which leads to high statistical errors.
Every time you have problem with your input script, you can go to the LAMMPS manual first. I can see from your input script, your Tdamp value for the fix nvt command is too low. I know your input script is from LAMMPS manual. In the manual, you are suggested to have Tdamp equal to 100*dt. So, it should be 50 in your case. In manual, it is stated that if Tdamp is too low, the temperature will fluctuate wildly.