Dear LAMMPS members,
I am struggling with a problem regarding the positive total potential energy of my system. I used 3 different force fields: Dreiding, COMPASS (class2), and OPLS. Lennard-Jones potential is used for pair potential and there is no electrostatic interaction. The total potential energy of my system which consists of hydrogen terminated nano-diamond cluster is in the following order for 3 different force fields:
1. COMPASS: -40000.0 kcal/mol
2. OPLS: +100000.0 kcal/mol
3. Dreiding: +200000.0 kcal/mol
The following table summarizes the contributions of each of bond stretching, angle bending and torsion into the potential energy (After 10000 steps with 1 fs time step and NVT ensemble).
Pot energy Pair energy Bond energy Angle Energy Torsion Energy
COMPASS -44065.206 8740.0453 5701.477 -36382.932 -22123.796
OPLS 83614.655 -11511.435 2083.1458 15501.265 77541.679
Dreiding 214964.88 8016.3129 2685.0546 13940.006 190323.5
I looked at the variation of potential energy of these three force fields vs. time. The energy was fluctuating around a constant value with very small amplitudes. I don’t know why I get positive potential energy with OPLS and Dreiding force fields while I got negative potential energy using COMPASS forcefield.
I got the list of bonds, angles and dihedrals using the TOPO tools in VMD.
Any help and feedback is greatly appreciated.
The best,
Farshad
Dear LAMMPS members,
I am struggling with a problem regarding the positive total potential
energy of my system. I used 3 different force fields: Dreiding, COMPASS
(class2), and OPLS. Lennard-Jones potential is used for pair potential and
there is no electrostatic interaction. The total potential energy of my
system which consists of hydrogen terminated nano-diamond cluster is in the
following order for 3 different force fields:
1. COMPASS: -40000.0 kcal/mol
2. OPLS: +100000.0 kcal/mol
3. Dreiding: +200000.0 kcal/mol
The following table summarizes the contributions of each of bond
stretching, angle bending and torsion into the potential energy (After
10000 steps with 1 fs time step and NVT ensemble).
Pot energy Pair energy Bond energy Angle Energy
Torsion Energy
COMPASS -44065.206 8740.0453 5701.477 -36382.932
-22123.796
OPLS 83614.655 -11511.435 2083.1458 15501.265
77541.679
Dreiding 214964.88 8016.3129 2685.0546 13940.006
190323.5
I looked at the variation of potential energy of these three force fields
vs. time. The energy was fluctuating around a constant value with very
small amplitudes. I don’t know why I get positive potential energy with
OPLS and Dreiding force fields while I got negative potential energy using
COMPASS forcefield.
I got the list of bonds, angles and dihedrals using the TOPO tools in VMD.
Any help and feedback is greatly appreciated.
<sigh> i feel like this has been explained at least 20 times this year
already... </sigh>
absolute energies have no meaning. only energy differences (for the same
potential/system) and - by extension - differentials/gradients, i.e.
forces, stress, etc.
also, different force fields have different strategies how they balance
between non-bonded and bonded energies and different functional forms.
axel.
Axel,
Thanks for your response. Actually, I had searched for the question I had and I couldn’t find anything relative to my issue in LAMMPS mailing list.
The next question I am going to ask is not really related to LAMMPS, rather it’s more related to Molecular Dynamics in general. So, I know I have to do some more in depth research about. I thought that the potential energy can tell me some good information about which force field I have to use for my system. But, based on your explanation, I have to consider some other factors to find out which force field is more appropriate for my system. These factors may include the topology details, the computational cost of the force field and so on. What advice and suggestion do you have for me in this matter?
The best,
Farshad
Axel,
Thanks for your response. Actually, I had searched for the question I had
and I couldn’t find anything relative to my issue in LAMMPS mailing list.
it is there. i have the impression that at least once a week somebody
explains to people that absolute energies have no meaning.
The next question I am going to ask is not really related to LAMMPS,
rather it’s more related to Molecular Dynamics in general. So, I know I
have to do some more in depth research about. I thought that the potential
energy can tell me some good information about which force field I have to
use for my system.
that sounds a bit like how some quantum chemists think. but even there it
is not always true. only if you solve the complete schroedinger equation
and for a complete (i.e. infinitely large) basis set.
But, based on your explanation, I have to consider some other factors to
find out which force field is more appropriate for my system. These factors
may include the topology details, the computational cost of the force field
and so on. What advice and suggestion do you have for me in this matter?
neither of those seem to be reasonable parameters. performance should be
similar for your choices (if not, let us know, there may be optimization
potential). what usually informs the choice of a force field is how well
important properties relativant to your research problem are reproduced. in
general, the simpler and the more general a force field, the less well it
works for a specific case and the less transferable its results are to a
variety of temperatures and environments (pressure, solvents).
difficult to say more without having more information.
axel.