VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Dec 01 2007 - 17:07:50 CST

Using VMD 1.8.6 and Membrane Plugin 1.1, I have built a 80x80A POPC membrane,
then embedded a protein in and minimized. That resulted in segmentation fault
after 12 minimization steps. Energy had decreased by seven orders of magnitude
and gradient by eigth orders of magnitude. Suspecting steric clashes, I found
many of them between water and lipid molecules at vdw overlap >= 0.6A.

Then I checked the original 80x80 membrane,finding 588 overlaps (at the above
vdw).

I have then built a smaller POPC membrane, 50x50A, though too small for my
protein. The intact membrane had 56 overlaps (at the above vdw).

I used defaults in building the membrane. Any suggestion where my mistake
resides?

Thanks
francesco pietra

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