From: Peter Jones (pm-jones_at_bigpond.com)
Date: Wed Jul 17 2013 - 22:06:10 CDT
Hi Thomas,
another option is to use a truncated octahedral periodic cell, which would have significantly less atoms than the enclosing cube,
PJ
On 18/07/2013, at 12:18 PM, Thomas Albers wrote:
> Hello!
>
> 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?
>
> Regards,
> Thomas
>
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