[gmx-users] Negative pressure in an interface NVT simulation
evanwlowry at gmail.com
Tue Sep 27 21:36:35 CEST 2016
How long is your simulation? Is it possible that it has not reached
On Tue, Sep 27, 2016 at 8:02 AM, Surya Prakash Tiwari <sptiwari at gmail.com>
> 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
> > Dear Gromacs users,
> > I am doing a water liquid-gas interface simulation in NVT ensemble (at
> > 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
> > Pres-ZZ -31.7913 0.0072 262.697 -0.0293928
> > #Surf*SurfTen 1151.56 6.5 1806.55 -21.4399
> > 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.
> > 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
> > 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.
> > my pressures are negative because the virial energies are larger in the
> > case of interface simulation compared to the case without interface,
> > 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
> > get the pressure right).
> > 5. Double the Z length of the gro file obtained in step 4. Use this as
> > 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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