# [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
>>
>>           ========================================
>>           --     gmx-users mailing list    gmx-users at gromacs.org
>>        <mailto:gmx-users at gromacs.org>
>>           <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>>
>>
>>           http://lists.gromacs.org/mailman/listinfo/gmx-users
>>           Please search the archive at http://www.gromacs.org/searchbefore
>>           posting!
>>           Please don't post (un)subscribe requests to the list. Use the
>> www
>>           interface or send it to gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>
>>           <mailto:gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>>.
>>
>>
>>
>>
>>    --     ========================================
>>
>>    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
>>
>>    ========================================
>>    --     gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>    Please search the archive at http://www.gromacs.org/search before
>>    posting!
>>    Please don't post (un)subscribe requests to the list. Use the www
>>    interface or send it to gmx-users-request at gromacs.org
>>    <mailto:gmx-users-request at gromacs.org>.
>>
>>
>>
> --
> ========================================
>
> 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
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.