Amit Choubey wrote:
On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul <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. 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.
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. Also recall that an NVE
ensemble represents a thermodynamically isolated system, not conducting heat or
engaging in work with the surrounding system. So any concept of external
pressure and equilibrating the pressure is irrelevant.
-Justin
amit
thank you
amit
On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Amit Choubey wrote:
Hi Everyone,
I was doing MD with SPC waters and found something which i am
not sure how to explain.
I made a box of SPC water of dimension 4x4x4 nm^3 and filled
with water using grenbox .
I then did a nvt simulation at 300 K for 1 ns . I used
berendsen
coupling and Reaction - Field for coulomb interaction.
Cut off
were all set to 1 nm. Temperature did converge to 300 K.
After
this i turned of nvt and did nve with RF-zero for another ns.
Energy was well converged during this (RMSD < 0.1 %).
Temperature was also around 304 K (RMSD < 1%). But the
pressure
was 1.1 Kilobar with a fluctuation of 20 % . I don understand
this, shouldnt this be around 1 bar ? Could some one suggest
whats on ?
Since an NVE ensemble employs neither a thermostat nor a
barostat, I
don't know why you'd expect that.
-Justin
Thank you,
amit
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
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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