[gmx-users] surface tension
katesedate at gmail.com
Mon Mar 14 23:57:06 CET 2011
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
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.
if you are interested in the surface tension of a pure liquid, which I
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
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
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.
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
> 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
> 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
> are equilibrated after 200ps, surface tension is not giving a constant
> value. Is that because I am not using berenden P coupling? (As mentioned
> 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
> 5- Does box six affect the results? (mine is 3.3 nm ).
> Thank you,
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