[gmx-users] Negative pressure in an interface NVT simulation
Surya Prakash Tiwari
sptiwari at gmail.com
Tue Sep 27 16:02:33 CEST 2016
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 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
> 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
> 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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