Exploding vdW energies in automatically generated POPC membranes

From: Lucas (lucasbleicher_at_gmail.com)
Date: Mon May 06 2013 - 15:33:47 CDT

Dear all,
I was trying to reproduce the membrane tutorial with my own protein,
but I kept running into the "Constraint failure in RATTLE algorithm"
error while trying to minimize the full solvated system with only the
lipid tails allowed to move. I have tried some suggestions I've found
in the archives for those errors to no success - energies always go
too high immediately, then at some point I get that error.

Some posts I've read said that automatically generated membranes
shouldn't result in clashes, so I kept looking elsewhere to see what
could be wrong, but after doing a few calculations using NAMD Energy,
it seems it really is all down to the membrane. If for example I run
the membrane builder with POPC, 160x160 size and c27 topology, and
then run NAMD Energy, I get this:

Frame Time Bond Angle Dihed
Impr Elec VdW Conf Nonbond
0 0 +28971.9 +59388.9 +24331.3
+341.334 -34635 +1e+10 +113033 +9.99997e+09

So it seems that even before I add anything else, van der Waals
energies are already too high. What am I doing wrong?

Best regards,

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