# [gmx-users] pressure for ambient water

Amit Choubey kgp.amit at gmail.com
Mon May 17 18:52:51 CEST 2010

```On Mon, May 17, 2010 at 6:45 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Amit Choubey wrote:
>
>>
>>
>> On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Amit Choubey wrote:
>>
>>
>>
>>        On Sun, May 16, 2010 at 5:15 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 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
>
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