Re: equilibration of "big" membrane

From: Richard Law (rlaw_at_llnl.gov)
Date: Sat Apr 07 2007 - 17:34:44 CDT

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
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