Hello Clemens,
> I read previously that for a system with Temp = 1. and mass = 1. a good
> value for the timestep is 0.01. I have Temp = 2.5 and mass1 = 20 and
> mass2 = 660. Is it correct to assume that I can scale the timestep
> inversely to the thermal velocity with a factor of (m / kT)^(1/2) ~ 3
> (using the mass1)? I have been using a timestep of 0.05 = 5e-15 s so far
> without any major problems.
In theory, yes. If you don't have any trouble with dt=0.05, I see no problem with that.
> The other parameter I am concerned about is gamma of the
> langevin-thermostat. So far I just used gamma = 1. = 10 ps^-1, which as
> I recently read is a little bit high. In my system I simulate a charged
> macromolecule with counter-ions in an implicit solvent (water). Is a
> value of gamma = 0.2 = 2 ps^-1 a good fit?
You typically just want to be in the overdamped regime for the ion motion. How far in there you are doesn't really matter. Trying to set "the right" value will fail anyways, because you are using the same gamma for particles that have different sizes and hydration shells in reality. Read [1] for a more thorough discussion of the relevant time and length scales.
Greetings,
Georg