Regarding way to compute only non-bonded forces on atoms using rerun command

LAMMPS LAMMPS General Discussion
1

Dear all,

I want to compute only non-bonded forces on atoms i.e. by excluding all the bonded interactions and also the intramolecular interactions. Can I do it by using the rerun command in LAMMPS?

I would be grateful for any suggestion.

Thank you.

Sanjeet

2

Yes. With rerun it reads the coordinates and then computes forces for whatever pair/bond/angle/dihedral/kspace/fix styles you have defined or not.

3

Dear Axel,

Thank you for your reply.

I have some other queries on the same line. Actually, I was just using the rerun command to verify the kinetic, potential, and total energy of my system with the original run. The potential energy of my system is in good agreement with the original simulation.

However, I observed that the kinetic energy and temperature of my system remains constant throughout the rerun simulation. I don’t know why?

Can you please suggest why it is so?

My original trajectory is generated using NVT simulation.

Thank you.

Sanjeet

4

With rerun you don’t have dynamics, you just advance the positions to the stored positions, so you cannot confirm the dynamics. For that you have to redo the simulation

Does your trajectory contain velocity data? and if yes, are you reading it with the rerun command?
If not, why should the kinetic energy change?

5

Dear Axel,

Thank you for the clarification. Now, its clear.

Thank you.

Sanjeet