On Mon, May 17, 2010 at 6:45 AM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Amit Choubey wrote: > >> >> >> On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Amit Choubey wrote: >> >> >> >> On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Amit Choubey wrote: >> >> Hi Justin, >> >> Since the density (1 gm/cc) and T (300 K) correspond to >> ambient >> condition, should not the equation of state dictate a >> pressure >> around 1 atm? >> >> >> If the equation of state involves temperature and pressure, yes. >> >> So if you fix the density and temperature shouldnt you land up >> with right pressure which we know should be 1 atm. >> >> >> You are not fixing (or conserving) the temperature in an NVE >> ensemble. That would be an NVT ensemble, employing a thermostat. >> >> I did do NVT first and then for sampling i removed the thermostat. Also as >> you mentioned there was not much difference b/n pressure values during NVT >> or NVE . The pressure value is as high as 1000 bar in both cases. >> >> >> Since instantaneous pressure is calculated (in part) from the >> kinetic energy, and since the kinetic energy is not guaranteed to be >> conserved, the pressure term will also fluctuate accordingly. >> >> >> This is correct. The pressure thus fluctuates about 20 % of the above >> mentioned value. >> >> >> http://www.gromacs.org/Documentation/Terminology/Pressure >> >> The internal energy of the system is constant in an NVE ensemble, >> the other terms may fluctuate as necessary such that all microstates >> occur with the same probability and the energy surface remains flat. >> >> I agree >> >> Also recall that an NVE ensemble represents a thermodynamically >> isolated system, not conducting heat or engaging in work with the >> surrounding system. >> >> true >> >> So any concept of external pressure and equilibrating the pressure >> is irrelevant. >> >> >> I am not trying to equilibriate the pressure. I am trying to measure the >> pressure. I also know that at 300 K and 1gm/cc the P should be 1 bar. >> >> Also, theoretically NVE or NVT are no different than NPT as far as >> measuring observables is concerned. Hence i was thinking that if you have >> the right volume density and temperature shouldnt you have the right >> pressure. >> > > I think the disconnect is arising because you're expecting a model of water > to behave almost like an ideal gas. The SPC water model, under NPT > conditions of 300 K and 1 bar, does not give the experimental density of > water; it is actually somewhat less than 1 g/mL. So constraining the system > to fit some pre-conceived notion of the volume to force the density to be > right conflicts with the properties of the water model itself. SPC wants to > be at a lower density, you're forcing it to be at a higher density, all > while fixing the volume of the simulation cell. Sounds to me like a recipe > for high pressure, since SPC wants to expand but you won't let it. > > So the starting configuration, assembled with the right density, has not > properly equilibrated under NPT conditions, yet you are expecting it to do > so when applying NVE conditions. I don't know that you'll ever be able to > satisfy all of these requirements simultaneously unless you can come up with > a better water model that replicates both ideal and real behavior :) > yes model is an issue too. I was just concerned about 3 orders of magnitude of difference in calculation of pressure. Thank you for the answering. amit > > -Justin > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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