AMBER Archive (2007)

Subject: Re: AMBER: Heat of Vaporization

From: Rita Cassia (Rita.Cassia_at_gmx.de)
Date: Wed May 16 2007 - 06:55:49 CDT

Dear Mr. Case,

thanks for the recommendation.

Regards

Rita

-------- Original-Nachricht --------
Datum: Tue, 15 May 2007 09:51:36 -0700
Von: "David A. Case" <case_at_scripps.edu>
An: amber_at_scripps.edu
Betreff: Re: AMBER: Heat of Vaporization

> On Tue, May 15, 2007, David A. Case wrote:
>
> > On Tue, May 15, 2007, Rita Cassia wrote:
> > >
> > > I would like to know how to do a md simulation with cutoff set to 0.
> >
> > What happens if you just try it? Comment out the section in mdread.f
> > that stops because this is "unreasonably small".
> >
>
> I just noticed that your subject said "Heat of vaporization". Setting the
> cutoff of zero would *not* be the way to compute a heat of vaporization.
> You need to to a separate simulation with a single gas-phase molecule to
> get
> the "gas" side of the equation.
>
> Here's a paper with a very nice discussion on how to compute heats of
> vaporization (it's harder than most people think!):
>
> %A H.W. Horn
> %A W.C. Swope
> %A J.W. Pitera
> %A J.D. Madura
> %A T.J. Dick
> %A G.L. Hura
> %A T. Head-Gordon
> %T Development of an improved four-site water model for biomolecular
> %simulations: TIP4P-Ew
> %J J. Chem. Phys.
> %V 120
> %P 9665-9678
> %D 2004
>
> If you want to go further, to get the vapor pressure and so on:
>
> %A H.W. Horn
> %A W.C. Swope
> %A J.W. Pitera
> %T Characterization of the TIP4P-Ew water model: Vapor pressure and
> boiling
> %point
> %J J. Chem. Phys.
> %V 123
> %P 194504
> %D 2005
>
> ...hope this helps...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

-- 
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten 
Browser-Versionen downloaden: http://www.gmx.net/de/go/browser
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu