[gmx-users] pressure for ambient water

[Amit Choubey]

On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul <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.

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>> 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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