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 <[email protected]> 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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