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 :)
-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
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