[SPAM] Can lammps compute the energy of each molecules in certain group?

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1

Dear Lammps users/developers,

Now, I want to get the total interaction energy of a certain molecule with all the molecules of a certain group. For example, if there is some H2O and some CH3COOH molecules in my system, I want to compute the total interaction energy of each H2O molecules with all the other CH3COOH molecules. Can LAMMPS do this?

Thanks!

Deng Chao

2

If by “total interaction energy”, you mean the per-atom

potential energy summed over the atoms in the molecule,

then yes. See the compute chunk/atom command and

define each chunk as a molecule (in your group).

Then use the fix ave/chunk command to sum the per-atom

energy over atoms in each chunk. You can also time average it.

If you want to exclude intra-molecule energies, I think you

would have to do the same thing but read snapshots from a previous simulation

with the rerun command and use a pair style where you

had turned off intra-molecular interactions.

Steve