equilibration of "big" membrane

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sat Apr 07 2007 - 13:49:05 CDT

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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