[gmx-users] lipid monolayer isotherm

[Hector Mtz-Seara Monne]

andre at qt.dq.ufscar.br wrote:

>On Mon, 17 Jan 2005, Hector Mtz-Seara wrote:
>
>  
>
>>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.
>>    
>>
>
>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
>
Can you tell me the typical value for gama_0 or 72 mN/m is a correct one?

>
>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.
>
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.
 

>maybe you could give some more details of your simulations: how did
>you assembled each monolayer? 
>
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.

>how long was each simulation run? 
>
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?

>if you plot surface area along the simulation time, is it stable?
>
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?

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

thank you in advance Hector.

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

>
>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
>
>/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
>
>  
>
>>thank you in avance, Hector.
>>
>>--------------------------------------------------------------------------------------------
>>
>>Hector Martinez-Seara Monne
>>
>>Universidad de Barcelona
>>Dept. Quimica Fisica
>>
>>hseara at netscape.net
>>--------------------------------------------------------------------------------------------
>>
>>
>>_______________________________________________
>>gmx-users mailing list
>>gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-request at gromacs.org.
>>
>>    
>>
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>  
>

-- 
Your favorite stores, helpful shopping tools and great gift ideas. 
Experience the convenience of buying online with Shop at Netscape! 
http://shopnow.netscape.com/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050117/e34f072c/attachment.html>