Re: equilibration of "big" membrane

From: Richard Law (rlaw_at_llnl.gov)
Date: Sun Apr 08 2007 - 19:21:34 CDT

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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