Dear Andre, Thanks for the helpful information.
I need to do some text reading to understand the periodic BC effect you are talking about. I dont see why increasing length in z direction does not lead to periodic BC in z and only for x, y ? does that mean the thickness of layer would be the Z dimension? then how much increase in one direction is reasonable? (If I have a 2 nm box). Also Can you please introduce some text book? Thank you, Best regards, 2011/3/15 André Farias de Moura <mo...@ufscar.br> > Dear Elisabeth, > > actually, it is the other way around, you need increase the box length in > one direction, thus keeping periodic boundary conditions in the other two > directions while a (infinitely periodic) surface is created. and notice > that > using genconf with -nbox 3 3 1 will increase your system but will not make > it a surface system, unless you increase the box length in one direction. > > as regards the size, the larger the model system, the smaller should be > the fluctuations. but mind that you should increase the size by a few > order of magnitude for any noticeable decrease on the (huge) RMSD > values you are getting. if you want to check the results for convergence > maybe you could try either a block averaging or a running average (grace > can do that for you). > > best regards > > Andre > > On Mon, Mar 14, 2011 at 7:57 PM, Elisabeth <katesed...@gmail.com> wrote: > > 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 <katesed...@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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