Dear Tian

I don't think the feature you are describing has not been added to

LAMMPS yet. (Langevin-dynamics in the zero-mass limit, or,

equivalently, in the infinite-friction limit. It is sometimes called

"Brownian Dynamics".)

http://en.wikipedia.org/wiki/Brownian_dynamics

If you want to add this feature to LAMMPS, that would be nice.

--- Summary ---

When I attempted to do this myself, but I ran into numerical

explosions and had to use small timesteps. I'm curious to know if by

now there are any good integration algorithms which avoid these issues

(other than using finite mass).

Feel free to skip the rest of this long email.

Andrew

--- Details: why I use finite mass Langevin Dynamics ----

I implemented this feature (zero-mass Brownian dynamics) in a

different MD program. However, in the end I decided not to use this

feature. Reducing the mass of each particle (to zero) results in much

faster, noiser motion. It causes causes particles to jump much

farther between timesteps (keeping the timestep fixed). Consequently

you have to use much smaller timesteps in order to prevent sudden

"jumps" in position which would cause numerical explosions. (This was

especially a problem using Lennard-Jones forces due to the 1/r^12

repulsion. Perhaps it's not a problem using harmonic forces.) I

suspect I'm not the only one who ran into this problem. Again, if

someone has a suggestion for a way around these kinds of problems,

please post it.

So I found it much more computationally efficient to use ordinary,

finite-mass Langevin dynamics (for example, as implemented using "fix

langevin" http://lammps.sandia.gov/doc/fix_langevin.html). I would

choose the damping time (the "tdamp" parameter) according to the

timescales of interest. (This is equivalent to choosing the mass, if

viscocity of the solvent is and particle size is already determined.)

For example, when I was running protein folding simulations,

movement of large domains of the protein were what mattered

physically, so I would set the damping time ("tdamp") similar to the

timescale of those kinds of motions. I did not care about what's

going on at shorter timescales than that.

I liked this paper:

D. K. Klimov, D. Thirumalai, "Viscosity Dependence of Folding Rates of

Protein", Phys. Rev. Lett., 79, 317-320 (1997)

My impression after reading that paper was if you increase the

friction coefficient (or equivalently reduce the mass) enough, then

the dynamics of protein folding are the same in that limit. (So you

don't have to go all the way to the zero-mass limit.)

I could be wrong, but I haven't really met anybody who is

passionate enough about this topic to correct me yet.