[gmx-users] surface tension in gmx

[Pedro Alexandre de Araújo Gomes Lapido Loureiro]

Hi,

 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface
> tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e
> Pres-XX-(bar),  Pres-YY(bar),  Pres--(bar)
>
> Can anyone tell me what the difference between these two is?
>
They should be equal, bearing in mind units conversion.


>
> 2- In pressure coupling settings there is surface_tension option which I
> guess is applicable where surface tension needs to be kept fixed. If one
> want to calculate surface tension I dont think this option make sense. Am I
> right?
>
Yes.

>
> 3- I am using the following setting: I calculate the average for a 2ns run
> and different start times as shown below. Although T, P and other quantities
> are equilibrated after 200ps, surface tension is not giving a constant
> value. Is that because I am not using berenden P coupling? (As mentioned in
> the manual surface tension works with berendsen)
>
> Pcoupl              =  Parrinello-Rahman
> Pcoupltype          =  isotropic
> tau_p               =  1      1
> compressibility     =  4.5e-5
> ref_p               =  40
>
>
> time period for which average is calculated   Average       RMSD
> Fluct.      Drift  Tot-Drift
>
> -------------------------------------------------------------------------------
> 1-2000 ps run: #Surf*SurfTen                    6.43844    3588.74
> 3588.35   0.091406    182.721
> 500-2000 ps    #Surf*SurfTen                   12.8518    3605.72
> 3605.26   0.132126    198.189
> 1000-2000ps   #Surf*SurfTen                    18.8821    3610.97
> 3610.8    0.11819    118.191
> 1500-2000ps   #Surf*SurfTen                     23.0072    3585.51
> 3584.93  -0.444037   -222.019
>
> This question is anything but trivial! Look at the RMSD values compared
with the averages. The dispersion is so high that you can't be sure if this
is or not equilibrated.



>
> 4- Assuming I am getting surface tension for a cubic box, to compare this
> with reported values in literature I need to divide by 6 (no. of surfaces)?
>
No. You have to divide by the number of interfaces (2 for a bilayer immersed
in water, for instance)



>
> 5- Does box six affect the results? (mine is 3.3 nm ).
>
> Yes, but see answer 3, above.


>
> Thank you,
>
>
>
>
>
>
>
>
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