Re: equilibration of "big" membrane

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Apr 09 2007 - 07:42:09 CDT

Well, this is what I should call "big" (not my tiny 150 x 150 A pet).

Michel

2007/4/9, Richard Law <rlaw_at_llnl.gov>:
>
>
> Great.
>
> Sorry - I meant 600 squared as in, 600A on each side - 3600A^2.
>
> Rich.
>
>
> On 4/8/07, L. Michel Espinoza-Fonseca < mef_at_ddt.biochem.umn.edu> wrote:
> >
> > 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
> > > >
> > >
> > >
> > >
> > > --
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++YNWA
> > >
> > > 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
> > > tel: +1 925 424 2338
> > > fax: +1 925 422 4665
> > > http://www.llnl.gov/bio/people/law/index.html
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >
> >
> >
> >
>
>
> --
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++YNWA
> 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
> tel: +1 925 424 2338
> fax: +1 925 422 4665
> http://www.llnl.gov/bio/people/law/index.html
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>

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