[lammps-users] Ensembles/MSD calculation in LAMMPS

Dear all,

I'm studying a bio-molecular system using different ensembles(NVE, NVT, and NPT). What method(algorithm) for each ensemble was used for LAMMPS? I think there are a lot of variations even for Nose-Hoover thermostat for NVT. Or would you let me know the references you(for developers) used to develop the codes, esp. for NPT simulation?

My another question is related to MSD in the NPT ensemble under periodic boundary condition which I asked a few weeks ago. I guess I've created a code which calculates MSD from LAMMPS output. But, I think there are two components(?) of MSD, one from the forces by the thermostat and one from the use of barostat. I think the displacement by the barostat should be neglected for true MSD calculation because it comes from some artificial(?) movement(dilation or contraction of the simulation box). I see that fix_msd can be combined with fix_npt to calculate MSD in LAMMPS. In that case how does it work for correct MSD calculation? It seems to me that the code uses the true displacement from current box size(including the displacement by the expansion or contraction of the box), which is contradictory to my understanding. Am I right or wrong? Or how can I correctly calculate MSD in the NPT ensemble?

Thanks in advance,

Dept. of Chem. Eng.
TAMU 3122 Texas A&M University
College Station, TX 77840


The NVT is standard Nose/Hoover. NPT is also Nose/Hoover, but follows these
2 papers for implementation in velocity-Verlet (the papers also discuss NH NVT).

Melchionna, S ; CICCOTTI, G ; HOLIAN, BL
Molecular Physics; 20 Feb. 1993; vol.78, no.3, p.533-44
Hoover NPT dynamics for systems varying in shape and size.

Explicit reversible integrators for extended systems dynamics.
Martyna, GJ ; Tuckerman, ME ; Tobias, DJ ; Klein, ML
Molecular Physics; 10 April 1996; vol.87, no.5, p.1117-57

Re: MSD with NPT. You are correct that fix msd does not account
for box dilation in computing the MSD. Rather it simply uses the atom’s
displacement from its original position. You would need to do something
fancier as a post-processing step, using the dump file box information,
to subtract out the dilation effects (which should be small if you are in
pressure equilibrium).