Dear Dr. Axel Kohlmeyer, Dr. Steve Plimpton, and LAMMPS Users,
Hello. First and foremost, I am deeply grateful for all of your responses to my inquiries on LAMMPS.
I was curious if I could ask a question regarding running Lennard-Jones potential under NPT Ensemble.
I currently have a simulation box that contains 100 polymer chains where the beads are connected via FENE potential and the non-connected beads are governed by the LJ potential with a cutoff of rc = 2.5. The spring constant for the FENE potential is 30 in LJ units.
When I ran this polymer chains under NPT ensemble to equilibrate the polymer chains where the initial/final temperature and pressure are set to 1.0 and 0, respectively, the MD simulation works perfectly fine. The Tdamp was set to 2.0
However, when I repeated this same simulation but I increased the final temperature to 3.0 while holding the pressure to 0, the NPT run encounters bad MD trajectory (FENE Bond too long)
The portion of my code is as follows:
fix 3 all npt temp 1.0 3.0 2.0 iso 0.0 0.0 10.0
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 2.5
I increased the temperature damping constant, Tdamp from 2.0 to 10.0 in order to damp the oscillations due to high temperature. I thought this oscillation might possibly be disturbing the FENE bonds. This alleviated the MD run such that the simulation was able to run for a longer time than the previous run. However, the FENE bond eventually elongated too much with a final error.
I would greatly appreciate if I could request for any other possible reasons that contributes to bad MD run during which the temperature increases from 1.0 to 3.0. Similar FENE bond too long error occurred when the temperature increases from 1.0 to 2.0 using NPT ensemble.
Thank you so much for your time.
Sincerely,
Masato Koizumi