[gmx-users] pressure in NVT simulations
ester.chiessi at uniroma2.it
Fri Apr 4 12:21:01 CEST 2003
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
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
e-mail: ester.chiessi at uniroma2.it
More information about the gromacs.org_gmx-users