From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue May 07 2013 - 00:17:36 CDT
Additionally you could try to turn off the fixed atoms, maybe there's
something wrong.
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: Norman Geist [mailto:norman.geist_at_uni-greifswald.de]
> Gesendet: Dienstag, 7. Mai 2013 07:16
> An: 'Lucas'
> Cc: Namd Mailing List (namd-l_at_ks.uiuc.edu)
> Betreff: AW: namd-l: Exploding vdW energies in automatically generated
> POPC membranes
>
> Hi Lucas,
>
> if you see energies looking like 999999.9999, you likely have
> superimposed atoms which the minimizer won't get rid of. Try to find
> the atoms causing the problem. Remember the periodic boundary
> condition. If your box is too small f.i., the wrapped atoms will
> superimpose at the box boundarys when the simulation starst.
> Additionally as I think your membrane is periodic in X and Y direction,
> and the ionize command, if you got ions, doesn't know that maybe, check
> if you have ions beside the membrane, that will be treated as wrapped
> into the membrane at simulation start, what would also cause
> superimposed atoms.
>
> Norman Geist.
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> > Auftrag von Lucas
> > Gesendet: Montag, 6. Mai 2013 22:34
> > An: namd-l_at_ks.uiuc.edu
> > Betreff: namd-l: Exploding vdW energies in automatically generated
> POPC
> > membranes
> >
> > 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
> > Total
> > 0 0 +28971.9 +59388.9 +24331.3
> > +341.334 -34635 +1e+10 +113033 +9.99997e+09
> > +1.00001e+10
> >
> > 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,
> > Lucas
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