Issue with redefining groups after displacement using displace_atoms (ReaxFF DNA simulation)

LAMMPS LAMMPS General Discussion
1

Hi everyone,

I’m running a DNA simulation using ReaxFF in LAMMPS. The strand has two fixed ends: the left side stays fixed, and the right side is stretched gradually using displace_atoms every few steps in a loop.

Due to step limits (100,000 steps per run), I use write_restart and continue the simulation with read_restart. After restart, I need to redefine the left_atoms and right_atoms groups. However, since atoms have been displaced, I can’t reliably recreate the same groups based on position.

Is there a recommended way to track or tag atoms through displacement and restart? Or a better strategy to define fixed-end groups that persist?

Thanks in advance for any help!

2

Why? They should be stored in the restart and restored when reading it back.
Check out the info groups command to confirm.

3

which reaxff potential(s) are you using ?

branch atoms lammps scm ref
water C/H/O/N/S/Mg/P/Na/Cu/Cl reaxff-monti2013a.ff CHONSMgPNaCuCl.ff Monti et al. 84
water C/H/O/N/S/Mg/P/Na/Cu/Cl reaxff-monti2013b.ff CHONSMgPNaCuCl_v2.ff Monti et al. 85
water C/H/O/N/S/Mg/P/Na/Cu/Cl/X reaxff-zhang2018.ff CHON2017_weak.ff Zhang and Van Duin86
water C/H/O/N/S/Mg/P/Na/Ti/Cl/F reaxff-huygh2014.ff CHONSMgPNaTiClF.ff Huygh et al. 87
water C/H/O/N/S/Mg/P/Na/Ti/Cl/F/Au reaxff-monti2016.ff CHONSMgPNaTiClFAu.ff Monti et al. 90
water C/H/O/N/S/Mg/P/Na/Ti/Cl/F/K/Li reaxff-ganeshan2020.ff CHONSMgPNaTiClFKLi.ff Ganeshan et al. 91

i dont remember any of them having the pi and pi-pi parameters trained well (if at all) so im very skeptical of any simulations results involving the rings structures of the dna bases.

P solvated parameters are suspicious also, long way to go there to get accurate physical results.

any new bio reaxff potential im not aware of ?