VMD-L Mailing List

From: Udeshini Manatunga (mana.udeshini919_at_gmail.com)
Date: Fri May 08 2020 - 03:46:25 CDT

Hi VMD users,

I'm a beginner to VMD and Lammps. I'm trying to simulate hydration reaction
between CaO and water using reaxff with lammps. I hope the water will break
into OH- and H+ during the simulation. I didn't define any bonds of the
water molecules as reaxff doesn't need bond details. I dump the lammps
trajectory file(.lammpstrj) and visualize it as follows,
1) When I visualize the trajectory file with psf file, I couldn't see any
bonds (I think this is because there are no bonds in the data file)
2) When I directly input the trajectory file, there is an extra bond
between H atoms in the water molecule.

So, How do I correctly visualize my system? Any reply would be
greatly appreciated. I attached the data file and the input file.


  • application/octet-stream attachment: system.in