Hello,<br>
<br>
Thank you for your answer. <br>
<br>
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?<br>
<br>
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. <br>
<br>
I appreciate any comments about number of molecules, box dimensions for such a study. <br>
<br>
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. ! <br>
<br>
Thanks for your time.<br>
Elisabeth<br>
<br>
******************************************<br>
<br>
if you are interested in the surface tension of a pure liquid, which I assume is<br>
true from your message, then you need to create at least one surface, since<br>
periodic boundary conditions make the model system infinite, i.e., without a<br>
surface whatsoever.<br>
<br>
the easiest way to make that happen is to increase the length of the box in<br>
one direction, say the z direction. that way you will end up with a system that<br>
resemble a (thin) liquid film with vacuum below and above, meaning that you<br>
now have two surfaces. run a regular simulation (NVT) e use g_energy to get<br>
the surface tension.<br>
<br>
btw: as any other pressure related property, fluctuations are huge.<br>
<br>
best<br>
<br>
Andre<br>
<br>
On Wed, Mar 9, 2011 at 12:25 PM, Elisabeth <<a href="mailto:katesedate@gmail.com" target="_blank">katesedate@gmail.com</a>> wrote:<br>
> Dear gmx users,<br>
><br>
> Since I am new to surface tension topic I need to ask very trivial<br>
> questions. Please help me out with these simple questions.<br>
><br>
> As a starting point I am going to calculate surface tension of a pure alkane<br>
> in a cubic box and compare with experimental values.<br>
><br>
> 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface<br>
> tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e<br>
> Pres-XX-(bar), Pres-YY(bar), Pres--(bar)<br>
><br>
> Can anyone tell me what the difference between these two is?<br>
><br>
> 2- In pressure coupling settings there is surface_tension option which I<br>
> guess is applicable where surface tension needs to be kept fixed. If one<br>
> want to calculate surface tension I dont think this option make sense. Am I<br>
> right?<br>
><br>
> 3- I am using the following setting: I calculate the average for a 2ns run<br>
> and different start times as shown below. Although T, P and other quantities<br>
> are equilibrated after 200ps, surface tension is not giving a constant<br>
> value. Is that because I am not using berenden P coupling? (As mentioned in<br>
> the manual surface tension works with berendsen)<br>
><br>
> Pcoupl = Parrinello-Rahman<br>
> Pcoupltype = isotropic<br>
> tau_p = 1 1<br>
> compressibility = 4.5e-5<br>
> ref_p = 40<br>
><br>
><br>
> time period for which average is calculated Average RMSD<br>
> Fluct. Drift Tot-Drift<br>
> -------------------------------------------------------------------------------<br>
> 1-2000 ps run: #Surf*SurfTen 6.43844 3588.74<br>
> 3588.35 0.091406 182.721<br>
> 500-2000 ps #Surf*SurfTen 12.8518 3605.72<br>
> 3605.26 0.132126 198.189<br>
> 1000-2000ps #Surf*SurfTen 18.8821 3610.97<br>
> 3610.8 0.11819 118.191<br>
> 1500-2000ps #Surf*SurfTen 23.0072 3585.51<br>
> 3584.93 -0.444037 -222.019<br>
><br>
><br>
><br>
> 4- Assuming I am getting surface tension for a cubic box, to compare this<br>
> with reported values in literature I need to divide by 6 (no. of surfaces)?<br>
><br>
> 5- Does box six affect the results? (mine is 3.3 nm ).<br>
><br>
><br>
> Thank you,<br>
>