Hi all,
I’m simulating the hydrated state of the polymer system (with water). I encountered the bond/atom missing errors at the beginning step or the middle steps (3000/150000fs or 131000/150000fs) depending on different parameters I tried to use. I have kept looking at some similar posts on the forum but still didn’t get it to work.
At first I used 0.5 and 1 fs timestep, the error came out at the beginning of the run. Then I used a smaller timestep, 0.2 fs, it could run a bit further. Previously I used the same MD protocol to simulate the anhydrous state of the polymer (without water molecule), it worked well and the outcomes were desirable. But the protocol didn’t work when I tried to add some water molecules to the system. I used tip4p/2005 water model and the shake command to constrain the water behaviours.
I have included the input file, polymer structure file (with 280 water molecules ), the log file and the error message. Since the total MD run took more than 2ns, I only included part of the MD cycle (50000fs nvt at 1000 degrees, 50000fs nvt at 300 degrees, and 50000fs npt at 300 and 2500 bar). The hydrated system contained 9488 atoms with water molecules randomly dispersing in the cell (757575 Angstrom) without overlaps. Any suggestion would be greatly appreciated!
diffusion.o7332302 (29.2 KB)
log.lammps (21.5 KB)
polymer_water.in (1.9 KB)
polymer_water.lmps (2.3 MB)
Many thanks,
Ajay