From: Lei Guo (leiguo_at_students.uiuc.edu)
Date: Thu Feb 19 2004 - 13:48:36 CST
Thanks for the detailed explanation. Now I am clear about this.
On Thu, 19 Feb 2004, [iso-8859-1] Jérôme Hénin wrote:
> > In fact, I am quite confused too. I'd like to know how to do NVT MD
> > in NAMD except using temperature rescaling method? (for example, it seems
> > that there is no Nose-Hoover method?)
> No, you're right, Nose-Hoover is currently not implemented. I'heard it is
> among the features they are willing to implement at some point, but if you
> want to know when, only Jim can answer that. But this leaves several
> different temperature control methods (apart from velocity rescaling) :
> * velocity reassignment, wich does not change the sampled thermodynamic
> ensemble, but perturbs the dynamics very strongly. This is the farthest you
> can be from Newtonian dynamics.
> * Benrendsen-like temperature coupling : coupling to a heat bath
> * Langevin dynamics
> > Also, please correct me if I am
> > wrong that if there is explicit solvent in simulation box, what would
> > lagevin dynamics mean? (I think lagevin dynamics has already taken into
> > accout the
> > interaction of solvent with solute, so if we use explicit solvent, we do
> > not use lagevin dynamics.)
> Initially Langevin dynamics was meant to model the effect of a solvent on a
> colloidal particle. But in NAMD, they use it in a very different context.
> Every atom (including explicit solvent) is applied a Langevin-like equation of
> motion, with the forces from the force field + a frictional term + a
> stochastic term. The Langevin force has no direct physical meaning here,
> since it doesn't represent interactions with an implicit medium.
> But it's an efficient way to add or remove energy to every atom and thus
> regulate the temprerature. Furthermore, the trajectories it produces sample
> from the canonical ensemble.
> What people usually do with NAMD is use Langevin dynamics with a rather small
> friction coefficient, to keep the temperature constant without affecting
> Newtonian motion too much. That way, you get a trajectory that is both
> realistic on short timescales and isothermal.
> Besides, the algorithm itself is robust and simple to implement.
> This whole Langevin idea is a bit weird at first, but with time, you get used
> to it. And when practicing it, you see that it just does the job. Well, most
> of the time.
> Is this what you wanted to know?
> In principio creauit Linus Linucem.
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