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

[Evan Lowry]

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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