[gmx-users] Negative pressure in an interface NVT simulation

[Surya Prakash Tiwari]

Hi Evan,

Thanks for answering. I ran for pretty long- 30 ns. I am sure that my
system has reached equilibrium. This is evident from the very small values
of Err.Est. and Tot-Drift of the pressure values included in my original
question. Any other hint!

Thanks.
​

On Tue, Sep 27, 2016 at 3:36 PM, Evan Lowry <evanwlowry at gmail.com> wrote:

> How long is your simulation? Is it possible that it has not reached
> equilibrium yet?
>
> Evan L.
>
> On Tue, Sep 27, 2016 at 8:02 AM, Surya Prakash Tiwari <sptiwari at gmail.com>
> wrote:
>
> > Hello again,
> >
> > Can someone take my question. You don't need to fully answer my question.
> > If you could just show me the direction, that would be more than enough.
> >
> > Thanks in advance.
> >
> > Surya Prakash Tiwari
> >
> > On Wed, Sep 21, 2016 at 12:11 PM, Surya Prakash Tiwari <
> sptiwari at gmail.com
> > >
> > wrote:
> >
> > > Dear Gromacs users,
> > >
> > > I am doing a water liquid-gas interface simulation in NVT ensemble (at
> > 298
> > > K, 1000 SPC/E, box size is described in the end). The pressure
> calculated
> > > (after equilibration) using gmx energy shows negative values:
> > >
> > > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> > > ------------------------------------------------------------
> > > -------------------
> > > Pressure                   -151.627       0.67    190.708    2.20173
> > (bar)
> > > Pres-ZZ                    -31.7913     0.0072    262.697 -0.0293928
> > (bar)
> > > #Surf*SurfTen               1151.56        6.5    1806.55   -21.4399
> > (bar
> > > nm)
> > >
> > > Since liquid and gas phases are in equilibrium, shouldn't pressure (at
> > > least Pzz) be equal to the saturation pressure of water. A large
> negative
> > > value is not making sense. Can someone help me with understanding this.
> > One
> > > of my colleagues used NAMD, and he said that he is getting the right
> > > pressure for the interface system!
> > >
> > > Though the pressures, I am getting, are negative; calculated surface
> > > tension value matches well with those available in the literature. It
> > seems
> > > that something is getting cancelled out, and I am getting the correct
> > > surface tension. Am I right?
> > >
> > > I tried to look how the pressure is calculated in Gromacs.
> > Mathematically,
> > > my pressures are negative because the virial energies are larger in the
> > > case of interface simulation compared to the case without interface,
> > other
> > > parameters remain almost same.
> > >
> > >
> > > The starting configuration for the NVT interface simulation was
> obtained
> > > using the following procedure:
> > > 1. 1000 water molecules were equilibrated using NPT ensemble (298 K, 1
> > > bar).
> > > 2. Find the average box lengths using gmx energy tool.
> > > 3. Obtain a gro trajectory file from the xtc/trr file using:
> > > gmx trjconv -f md -s md.tpr -o conf.gro -pbc whole -b 1000
> > > 4. A snapshot configuration from the above gro file was chosen such
> that
> > > its box lengths matches with the average box lengths obtained in step 2
> > (to
> > > get the pressure right).
> > > 5. Double the Z length of the gro file obtained in step 4. Use this as
> > the
> > > starting configuration for NVT interface simulation.
> > >
> > >
> > > I have tried to explain as much as possible to get the help, but if I
> am
> > > missing some information, please let me know and I will provide that.
> > >
> > >
> > > Thanks a lot. I look forward for some help.
> > >
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