From: Thomas Albers (talbers_at_binghamton.edu)
Date: Wed Jul 17 2013 - 21:18:16 CDT
I have got a system with a 400 amino acid dimer that fits into a
128*96*96 A oblong water box. That's about 100K atoms. A cubic
128*128*128 water box would be about 200K atoms.
If I restrain the rotation of the protein with an orientation colvar,
as hinted at on p. 123 of the NAMD 2.9 manual there's a *substantial*
speed penalty; IIRC it's so bad that I might as well drop the colvar
and use a cubic box instead. However, in the recent protein-ligand
binding tutorial (this one:
http://www.ks.uiuc.edu/Publications/Stories/plbtutorial/) the colvar
is defined only for the backbone of the protein, this is much faster,
but I fear I might introduce bias in the internal degrees of freedom.
Does anyone on the list have some input?
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