Molecular statics calculations in LAMMPS for two hydrogen molecules?


I’m trying to run a molecular statics calculation in LAMMPS for the generation of intermolecular potential energy curve for H2-H2 interaction (i.e., two hydrogen molecules in different L, T, parallel, and crossed configurations) and compare to the ones calculated using ab initio methods. What would be the best way to build the structure for the LAMMPS input file and run the simulation? Should I perform a 2D simulation? Define a region or box? What boundary conditions?


Best Regards,

Sasan Nouranian, Ph.D.

Postdoctoral Associate

Center for Advanced Vehicular Systems

Mississippi State University

Office 2147

200 Research Boulevard

Starkville, MS 39759

Office Phone: (662) 325-7316

Cell Phone: (662) 347-0606

E-mail: [email protected]…1024…

Well, since nobody else has answered this yet, I'll make an attempt.

I know what other people are going to say:
It sounds like the first thing you need to do is think about what
kind of force-field you want to use.

It's an understandable mistake because some simulation programs
come with other programs (if I understand correctly, like AMBER's leap
and antichamber) which automate the hard work of picking the
force-field parameters for you. LAMMPS allows you the freedom to pick
those parameters manually.

In the simplest case, when you are not forming or breaking bonds, a
traditional MD force field would treat hydrogen atoms as simple
Lennard-Jones spheres connected by rigid, fixed-length rods. In that
case, you only need 2 parameters: the "epsilon" and "sigma" parameters
of the Lennard-Jones interaction, which you must choose by looking at
the available literature. (...or steal from other popular force
fields. AMBER's GAFF comes to mind.)

Anyway, once you know what force-field you want to use, and you
know the pairwise potential energy between each hydrogen atom U(r), it
seems like you could easily use excel, or awk, or a simple for-loop in
some scripting language to sum up U(r) between these 4 atoms, for
different separation distances. If instead you want to use LAMMPS to
do this, then I suppose you would need to learn the LAMMPS data file
format, or a trajectory/dump file format (it's not hard), and write a
short file for a 4-atom system, load it in LAMMPS and compute the
energy, but that seems like unnecessary work for your system, unless
I'm oversimplifying it.

Hope this helps.