[gmx-users] Re: surface tension
katesedate at gmail.com
Tue Mar 15 05:52:39 CET 2011
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?
2011/3/15 André Farias de Moura <moura at 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
> 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
> On Mon, Mar 14, 2011 at 7:57 PM, Elisabeth <katesedate at gmail.com> wrote:
> > Hello,
> > Thank you for your answer.
> > 1- If I am right I have to increase the length in two directions rather
> > 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
> > 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
> > 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,
> > 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
> > one direction, say the z direction. that way you will end up with a
> > that
> > resemble a (thin) liquid film with vacuum below and above, meaning that
> > now have two surfaces. run a regular simulation (NVT) e use g_energy to
> > 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
> >> 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.
> >> I
> >> right?
> >> 3- I am using the following setting: I calculate the average for a 2ns
> >> 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
> >> 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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