[gmx-users] Re: surface tension
André Farias de Moura
moura at ufscar.br
Tue Mar 15 17:38:41 CET 2011
Dear Elisabeth,
PBC are still there when you increase the box length in one direction, but that
increase creates an empty region between the periodic images. provided the
empty region is large enough (larger than cutoff values, for
instance), periodicity
no longer affects the system during a typical MD simulation, except
for the other
two directions.
as regards long range corrections, either do not use them at all or choose a two
dimensional correction (see the manual).
and try some google search on the simulation of Langmuir films. for instance, I
wrote this paper a while ago:
Molecular Dynamics Simulation of a Perylene-Derivative Langmuir Film
André F. de Moura and Milan Trsic
J. Phys. Chem. B, 2005, 109 (9), pp 4032–4041
DOI: 10.1021/jp0452711
best
Andre
On Tue, Mar 15, 2011 at 1:52 AM, Elisabeth <katesedate at gmail.com> wrote:
> 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 <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
>> 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 <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
>> > 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 <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
>> >> 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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