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.