[gmx-users] pressure for ambient water

[Justin A. Lemkul]

Amit Choubey wrote:
> 
> 
> On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at 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
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto: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> <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

========================================