[gmx-users] surface tension in gmx

[André Farias de Moura]

regarding your first question, the definition of gamma is not
correct, you are getting energy/length⁴ instead of energy/area
(multiply by Lz instead of dividing by it)


2011/3/9 Pedro Alexandre de Araújo Gomes Lapido Loureiro <palaplou at gmail.com>:
> 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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>
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