[gmx-users] pressure for ambient water
Amit Choubey
kgp.amit at gmail.com
Mon May 17 05:12:24 CEST 2010
On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul <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>> 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.
>
> -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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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