From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon Feb 13 2012 - 09:59:18 CST
Felipe,
"correct" dynamics is a matter of definition and what you are trying to
describe or achieve. TIP3P is a model for water as you state it.
I usually use Langevin with 1 ps^-1 and forget about the rest.
Gianluca
On Mon, 13 Feb 2012, felmerino_at_uchile.cl wrote:
>
> Dear NAMD users,
>
> Lately in the lab we have been discussing about which thermostat use in our simulations. I
> know this can be just a detail, but it is quite tricky. The velocity rescaling method will
> not give he correct ensemble, but the langevin dynamics will affect the dynamics of the
> system and in principle quantities such as diffusion constants will be modified. For NVT
> simulations the Lowe-Andersen thermostat should be the option to avoid that, but we are
> doing NPT and the Langevin barostat already modifies the dynamics (it contains a
> "thermostat on its own right?).
>
> Besides, as far as i remember the TIP3 water model (the one we are using) already has a
> higher diffusion constant and the langevin damping coefficient is used to somehow match it
> to the experimental value, so i do not know if it is possible to obtain the "correct"
> dynamics with TIP3 water and any ?Galilean invariant? thermostat.
>
> Does anyone have any insights on this topic?
>
> regards
>
> Felipe
>
>
>
>
>
-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:38 CST