[gmx-users] pressure in NVT simulations

[Ester Chiessi]

David van der Spoel wrote:

> On Thu, 2003-04-03 at 14:00, Ester Chiessi wrote:
> >
> >
> > David van der Spoel wrote:
> >
> > > On Thu, 2003-04-03 at 10:08, Ester Chiessi wrote:
> > > > Hi ,
> > > >
> > > > I have a doubt. Are pressure values meaningful in NVT molecular dynamics
> > > > simulations?
> > > > I 'm obtaining pressure values around (1000 +/- 1000) bar.
> > > >
> > > yes, that means your density is too high (unless you want high
> > > pressure...)
> > >
> >
> > Calculated by g_density total density is 1.01483 g/cm3. Partial densities
> > across box range from 0.97 to 1.05 g/cm3.The system to simulate is a hydrogel
> > 10% w/v at 303 K.
> I'm not sure g_density is correct, does it use the mass in the tpr file?

I suppose so.

> Otherwise editconf might compute it for you.
>
> What should the density be?

Experimental density is not very different from that of pure water. Calculated (by
hand) density for the simulated system is 1.01 g/cm3.
When I solvated the polymer by genbox, I obtained 1.0711g/cm3 and the same value
was given by editconf.
The more confident value seems that by g_density.


> >
>
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel,        Dept. of Cell & Mol. Biology
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
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--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
       39*6*72594874
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