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<a class="moz-txt-link-abbreviated" href="mailto:andre@qt.dq.ufscar.br">andre@qt.dq.ufscar.br</a> wrote:<br>
<blockquote type="cite" cite="mid20050117144503.S47163-100000@qt.dq.ufscar.br">
<pre wrap="">On Mon, 17 Jan 2005, Hector Mtz-Seara wrote:
</pre>
<blockquote type="cite">
<pre wrap="">I've been running several test dynamics and I'm really confused. In
general the surface tensions that gromacs gives me are much higher than
experimental ones, many times more than 3 times (I know that to have in
mN/m units I have to divide by 10 and by two for the two monolayers) and
it means that they are higher than experimental water, 72mNm( someone
knows the surface tension of the SPC water that is in gromacs??), but
what is really annoying me is that in theory the surface tension of a
fatty acid monolayer goes down when the concentration of the lipid in
the monolayer goes up but the results seem to be the opposite, and I say
"seems" because sometimes the same dynamic brings me to different
equilibrium surface tension or area/lipid ( it happens in both ensembles
I use TNAhz and TN(st)hz). If anyone can give me any clue why I been
having all this problems and if there's any way to solve them, I'll be
so pleased.
</pre>
</blockquote>
<pre wrap=""><!---->
g_energy output gives surface pressure, not surface tension. dividing the
result by 20 just changes the units from bar nm to mN/m. to compute the
surface tension you have to use the standard expression:
gama = gama_0 - pi
where:
gama = surface tension
gama_0 = pure water surface tension</pre>
</blockquote>
Can you tell me the typical value for gama_0 or 72 mN/m is a correct one?<br>
<blockquote type="cite" cite="mid20050117144503.S47163-100000@qt.dq.ufscar.br">
<pre wrap="">
pi = surface pressure
anyway, if you're getting surface pressures 3-fold larger than that
of pure water, then your surface tension is negative, isn't it? if
that happens to be the case, then your systems may be still away
from mechanical equilibrium.</pre>
</blockquote>
In fact the typical value of the surface pressure that gromacs is given me
is between 100 -150 and then when I use it them to calculate the surface
tension it is negative. To obtain this values I run several dynamics with
different occupations for azobenzene from 25 A²/molec to 50 ²/molec where
25 is the minimum where the monolayer breaks, and after 40 the monolayer
presents some holes and for Arachidic Acid dynamics from 20 A²/molec to
40 A²/molec. The monolayers I started working with where build by two monolayers
with 625 lipids in every side and dynamics were done till times up to 6ns
writing every 10ps the information. Now I'm working with smaller system sizes
till the results are not going ok, 100 lipid per side and they are run 2ns.<br>
<br>
<br>
<blockquote type="cite" cite="mid20050117144503.S47163-100000@qt.dq.ufscar.br">
<pre wrap="">
maybe you could give some more details of your simulations: how did
you assembled each monolayer? </pre>
</blockquote>
The monolayer was constructed with a program that I make myself (using the
gromacs utilities) which allow you to construct any system you like only
leaving a little space between the lipids and the water. To avoid this problem
and bad contact I always minimize the structure till the precision machine
( single precision), and finally I run the dynamics. <br>
<blockquote type="cite" cite="mid20050117144503.S47163-100000@qt.dq.ufscar.br">
<pre wrap="">how long was each simulation run? </pre>
</blockquote>
I run it from 2ns to 6ns, and the problem is that de surface tension seems
to be stable till nearly the beginning and the as the pressure oscillate
so much is difficult to advertise any tendency different to a statistical
one. There's any criterion to know if I have my system in a stable state?<br>
<blockquote type="cite" cite="mid20050117144503.S47163-100000@qt.dq.ufscar.br">
<pre wrap="">if you plot surface area along the simulation time, is it stable?</pre>
</blockquote>
The point is normally. I wasn't still able to stabilize box size in the TN(st)hz
ensemble, even differents Tau_p changes the behavior of the system, (which
do you use, Tau_p=0,1 is okay or is better a higher one, in that case which?
what about the compressibility, I always put the default of the water is
it correct?<br>
<br>
Sorry for all of that questions but I'm really lost, and I haven't enough
experience to get out of this hole, If you need more information just ask
I'll be glad of given you as much as you need if it can be the solutions
of my nightmares<br>
<br>
thank you in advance Hector.<br>
<br>
PD. I can remember that you answered some of my questions about monolayer
in the past and I the last one you told me that you was going to publish
a paper of an isotherm or a very related topic, have you already done if
yes please I would like to see it thank. Maybe I'm wrong in this case sorry<br>
<blockquote type="cite" cite="mid20050117144503.S47163-100000@qt.dq.ufscar.br">
<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="">thank you in avance, Hector.
--------------------------------------------------------------------------------------------
Hector Martinez-Seara Monne
Universidad de Barcelona
Dept. Quimica Fisica
<a class="moz-txt-link-abbreviated" href="mailto:hseara@netscape.net">hseara@netscape.net</a>
--------------------------------------------------------------------------------------------
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</blockquote>
<pre wrap=""><!---->
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