[gmx-users] surface tension

[Elisabeth]

Hello,

Thank you for your answer.

1- If I am right I have to increase the length in two directions rather than
one, to create a plane parallel to XY for example?

2- Can you please give me an idea on how many molecules I need to have in
the box and also what should be the thickness of layer? I have now 3nm X 9 X
9 dimensions. That is thickness of 3nm. What I did was replicating a 3nm box
using genconf -nbox 3 3 1. I dont know what is the correct way of creating a
layer for surface tension calculation.

I appreciate any comments about number of molecules, box dimensions for such
a study.

3- my last question is how can I make sure surface tension reported by
g_energy is the equilibrated one. RMSD is very big compared to surf. ten. !

Thanks for your time.
Elisabeth

******************************************

if you are interested in the surface tension of a pure liquid, which I
assume is
true from your message, then you need to create at least one surface, since
periodic boundary conditions make the model system infinite, i.e., without a
surface whatsoever.

the easiest way to make that happen is to increase the length of the box in
one direction, say the z direction. that way you will end up with a system
that
resemble a (thin) liquid film with vacuum below and above, meaning that you
now have two surfaces. run a regular simulation (NVT) e use g_energy to get
the surface tension.

btw: as any other pressure related property, fluctuations are huge.

best

Andre

On Wed, Mar 9, 2011 at 12:25 PM, Elisabeth <katesedate at gmail.com> wrote:
> Dear gmx users,
>
> Since I am new to surface tension topic I need to ask very trivial
> questions. Please help me out with these simple questions.
>
> As a starting point I am going to calculate surface tension of a pure
alkane
> in a cubic box and compare with experimental values.
>
> 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?
>
> 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?
>
> 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
>
>
>
> 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)?
>
> 5- Does box six affect the results? (mine is 3.3 nm ).
>
>
> Thank you,
>
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