[gmx-users] Negative pressure in an interface NVT simulation
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 29 08:16:42 CEST 2016
On 27/09/16 16:02, Surya Prakash Tiwari 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.
This is as it should be. Your system has a surface tension as you see
that you can compare to experimental data if you wish. Since you have
two surfaces you have to divide the number by 2 and correct for units.
Check J. Chem. Theory Comput. 11 pp. 2938-2944 (2015) for an up to date
discussion of surface tensions in simulations.
> 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.
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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