From: Lei Guo (leiguo_at_students.uiuc.edu)
Date: Thu Feb 19 2004 - 13:12:01 CST
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?) 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
interaction of solvent with solute, so if we use explicit solvent, we do
not use lagevin dynamics.)
On Thu, 19 Feb 2004, [iso-8859-1] Jérôme Hénin wrote:
> > In the tutorial for NAMD, the example involves solvating a protein in a
> > waterbox and using Langevin to control temperature and pressure. Is this
> > langevin dynamics / molecular dynamics ?
> In short : yes, it is Langevin dynamics.
> > Can anyone please explain !
> The topic is quite broad. I don't think anyone will give you a course on how
> to do constant-temperature MD by mail, on this mailing-list. Could you be
> more specific on what kind of explanations you want ?
> We'll be happy to help.
> Jérôme Hénin
> Equipe Dynamique des Assemblages Membranaires
> Université Henri Poincaré / CNRS UMR 7565
> B.P. 239 54506 Vandoeuvre-lès-Nancy Cedex
> Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 71
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