Dear All,
I am trying to calculate per atom energy using compute pe/atom. I am interested in computing vdw energy of each water molecule. I have used following keyword to find it -
“compute vdw all pe/atom pair”
Since LJ parameter for hydrogen is zero in my data file, I expect pair energy for hydrogen should be zero but I am getting a non-zero value for pair energy, Does pair energy involves some other contribution as well?
Thanks
Hydrogen in water potentials have a nonzero charge. Axel
Thanks Dr. Axel.
It means pair energy has contribution from both Coulomb and LJ(general Lammps notion). Is there way just to separate out vdw contribution. In that case what does Kspace keyword specifies ? Is it the contribution to the electrostatic interaction coming from kspace only or total electrostatic energy?
When I sum energy from kspace and pair I get the correct energy of each water molecule.
Thanks Dr. Axel.
It means pair energy has contribution from both
Coulomb and LJ(general Lammps notion).
yes, of course! you did specify lj/cut/coul/long
or some variant of it as pair style, didn't you?
Is there way just to separate out vdw contribution.
not during the simulation. you can use the rerun
feature and evaluate the energies using a data file
with all charges set to zero or using lj/cut only
as pair style.
In that case what does Kspace keyword specifies ? Is it the
the part of the coulomb that is dampened out in real space.
i recommend you read up on how ewald summation and
equivalent schemes work in your favorite MD text book.
contribution to the electrostatic interaction coming from kspace only or
total electrostatic energy?
this is self-explanatory once you caught up on ewald summation.
When I sum energy from kspace and pair I get the correct energy of each
water molecule.
as you are supposed to.
axel.