Re: equilibration of "big" membrane

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sun Apr 08 2007 - 14:02:44 CDT

Hi Richard,

Thank you for your suggestions. It seems that is working well now. The
problem was probably related to the fact that the no. of water molecules was
insufficient, causing some artificial interactions within the bilayer.

Cheers,
Michel

2007/4/8, Richard Law <rlaw_at_llnl.gov>:
>
> I've equilibrated membranes up 600A^2 with no problem. You shouldn't need
> so many minimization steps but start the equlibration at 0 and heat with the
> temp bath only. If you still can't get it to work try using the berendsen
> pressure coupling rather than langevin for a few picoseconds while things
> settle down. Make sure you have enough water on each side.
>
> Rich.
>
>
> On 4/7/07, L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu> wrote:
> >
> > Hi guys,
> >
> > I was wondering if any of you have observed a similar problem. I built
> > a 130 x 130 A POPC bilayer using the membrane plugin of VMD. Then I
> > subjected such membrane to energy minimization and heating (keeping
> > the heads constrained). No problem then. But immediately after the
> > volume equilibration (with the heads constrained), NAMD aborts
> > complaining about a failure in the RATTLE algorithm. I've been redoing
> > it, increasing the minimization steps up to 30,000 and slowly
> > increasing the temperature, and I got the same thing. I have to
> > mention that I've built membranes of several sizes (up to 100 X 100 A)
> > and by using the same procedure everything goes well.
> >
> > Now my question is: have any of you observed some problems at
> > equilibrating "big" bilayers? All comments would be really
> > appreciated.
> >
> > Thanks,
> > Michel
> >
>
>
>
> --
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>
> Dr. Richard J. Law
> Biosciences & Biotechnology Division
> Chemistry, Materials and Life Sciences Directorate
> Lawrence Livermore National Laboratory
> L-372, 7000, East Ave,
> Livermore.
> CA. 94550 USA
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