[gmx-users] lipid monolayer isotherm
Andre Farias de Moura
andre at qt.dq.ufscar.br
Tue Jan 18 12:02:58 CET 2005
I can't see anything strange in the details you gave so far: your
system is large, much larger than I'm used to work with, and that's
not a problem at all, it's a good approach, I think. besides, the
length of your simulations should be enough to relax pressure and
area, I usually get stable average values after ca. 500 ps.
maybe it has something to do with the way you set up the monolayers.
if I got the point, you (1) assemble two monolayers, (2) add water
molecules and (3) run some minimization runs to relax bad contacts.
that's the way I first tried to assemble my model systems and I soon
realized that they wouldn't attain mechanical equilibrium within a
few nanoseconds if the initial structures were too far from the
equilibrium structures. you may try to pick up one monolayer and
treat it as a single crystal, using 3D PBC, then run some simulated
annealing runs, coupling the system to an anisotropic pressure bath
with all off-diagonal compressibilities set to zero. you should get
a monolayer that resembles the 2D solid phase of a Langmuir film.
replicate it, translate the replica using gmx tools and add water
molecules between the two layers.
you may increase the surface area by removing some molecules from
each monolayer (allways keep the same number on each monolayer!)
On Mon, 17 Jan 2005, Hector Mtz-Seara Monne wrote:
> 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?
try any running average scheme to filter the high frequency noise, if
you couple your system to a surface pressure barostat then the average
should level off after a while.
> >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?
I allways use tau_p = 1.0 ps and standard water compressibility. besides,
I couple each monolayer to a different heat bath (and water molecules are
coupled to another reservoir).
> 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
the paper has been just accepted for publication in the JPC, I'll send
you a copy as soon as it is available.
Dr. Andre' Farias de Moura
Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
Sao Carlos - SP - Brasil
Grupo de Quimica Quantica
Instituto de Quimica de Sao Carlos
Universidade de Sao Paulo
Sao Carlos - SP - Brasil
> >best regards,
> > 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
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