[gmx-users] pressure for ambient water

Justin A. Lemkul jalemkul at vt.edu
Mon May 17 02:15:10 CEST 2010

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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.  Sounds like
you want to be using an NPT ensemble, not NVE.  For NVE, your volume and energy
are conserved, so there should (in theory) be little deviation from whatever

-Justin

> thank you
> amit
>
> On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at 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> | (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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