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Thanks Andre, for your answer, but only one more short question the
presence of vacuum doesn't affect in the result of the surface tension
as is calculated in gromacs as it uses de z box size,Lz? and in wich
units are the result because it give me numbers up to 3000 for my
system which I can't compare with experimental ones?<br>
<br>
My e-mail is: <a class="moz-txt-link-abbreviated" href="mailto:hseara@netscape.net">hseara@netscape.net</a> for the paper<br>
<br>
Thank you, hector<br>
<br>
Andre Farias de Moura wrote:
<blockquote cite="mid20041201101317.R31425-100000@qt.dq.ufscar.br"
type="cite">
<pre wrap="">hi hector,
On Wed, 1 Dec 2004, Hector Mtz-Seara wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Thank you very much Andre, my system has two monoloyers one on each
side. Do you think that the way of calculate surface tension of gromacs
is accurate enough I haven't found so much information about how it's
evaluated inside the package, if not how do you make the measure?
In advance hundreds of thanks was very useful your answer.
</pre>
</blockquote>
<pre wrap=""><!---->
I wouldn't say it's accurate, pressure calculations are inherently
noisy, very noisy, but g_energy uses standard procedures to calculate
the surface tension from energy output (take a look at the manual in
the surface tension coupling section). although noisy, average values
are consistent if your simulations are properly set up.
</pre>
<blockquote type="cite">
<pre wrap="">( have you any paper with your isotherms????)
</pre>
</blockquote>
<pre wrap=""><!---->
I've just submitted a paper to the J. Physical Chemistry, I'll send
you a copy as soon as it's into final form.
</pre>
<blockquote type="cite">
<pre wrap="">Hector
</pre>
</blockquote>
<pre wrap=""><!---->
best regards,
andre'
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Dr. Andre' Farias de Moura
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
Sao Carlos - SP - Brasil
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Endereco Atual
Grupo de Quimica Quantica
Instituto de Quimica de Sao Carlos
Universidade de Sao Paulo
Sao Carlos - SP - Brasil
Telefone: 55-16-3373-8055
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
</pre>
<blockquote type="cite">
<pre wrap="">
Andre Farias de Moura wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Hector,
I couple of months ago I posted a message saying that NVT
was OK to simulate monolayers but it seems to me now that
there may be some regions in lipids isotherms where non-
equilibrium (metastable) states occur. surface-tension is
certainly a better coupling than NVT for monolayers, you
just need to set compressibility to zero in the direction
perpendicular to the interface to avoid the system
collapse you mentioned.
by the way, if I understood your system setting, you're
using only one lipid monolayer on one side of the water
slab, the other side being a water/vacuum interface. it
seems to me that you should use one monolayer on each
side of the water slab, see the work of Ahlstrom and
Berendsen J. Phys. Chem. 97 (1993) 13691. if you don't,
your surface pressure will have both a water surface
tension contribution and the water/lipid interfacial
tension, I don't think that these contributions can be
separated.
I hope it helps,
best regards,
andre'
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Dr. Andre' Farias de Moura
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
Sao Carlos - SP - Brasil
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
Endereco Atual
Grupo de Quimica Quantica
Instituto de Quimica de Sao Carlos
Universidade de Sao Paulo
Sao Carlos - SP - Brasil
Telefone: 55-16-3373-8055
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
On Mon, 29 Nov 2004, Hector Mrz-Seara Monne wrote:
</pre>
<blockquote type="cite">
<pre wrap=""><a class="moz-txt-link-abbreviated" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On Mon, 2004-11-29 at 12:05 +0100, Hector Mrz-Seara Monne wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi all,
We are simulating monolayers. Our system is based in the next configuration:
VACUUM
------
LIPID
------
WATER
------
VACUUM
in the literature we have found two mainly different ensembles to work with monolayers simulations,
the first NVT which works perfectly and the second NPnT( surface tension ) which in our simulations the
vacuum disappeared because the Berendsen pressure algorithm scales the box till the box surrounds
perfectly the system without vacuum,after a few dynamic steps, which means that we have interaction of
the lipids and the water across the box by the periodic boundary conditions.
</pre>
</blockquote>
<pre wrap="">You only should scale the X en Y coordinates of the box (in the plane of
the lipids).
</pre>
</blockquote>
<pre wrap="">Then it means that you can't use NPnT( surface tension ) ensemble and
the correct one is NVT or NA( surface tension )T, it is
correct or there is something that I'm not understanding? It's just that
the article that I mention confuses me
</pre>
<blockquote type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">The problem is that in the article, Biophysical Journal;Volume 82;2511-2519, it seems that Dr. Feng Sun
is using the second ensemble without loosing the vacuum because he uses periodic boundary conditions, and
water and lipids do not interact across the box. The package he use is charm. Someone knows if the algorithm
of Charmm for the pressure bath is different from gromacs's one and don't scale the box the box, allowing you
to have vacuum in both sides of the monolayer while normal pressure, Pn, is applied to the bulk system. If not
how anyone can use NPnT(surface tension) ensemble for simulating monolayers? Is correct to use NVT ensemble
in order to build an isotherm?
Thank you, Hector
--------------------------------------------------------------------------------------------
Hector Mart�nez-Seara Monn�
Universidad de Barcelona
Dept. Qu�mica Fisica
<a class="moz-txt-link-abbreviated" href="mailto:hseara@netscape.net">hseara@netscape.net</a>
--------------------------------------------------------------------------------------------
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