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About car efficiency... (and re: Skippy and Tyop)	by etwas_egal	2007-04-30 00:07:38
Consolidate errands	by shadowboy813	2007-04-30 06:06:51
Refinement to point 6: accelerate slower.	by etwas_egal	2007-04-30 07:46:13
No, I meant DRIVE slower for point 6	by shadowboy813	2007-04-30 10:12:30
Highway speed limits here are at your break point	by etwas_egal	2007-04-30 11:34:10
Any clustering I'm currently doing...	by shadowboy813	2007-04-30 14:20:21
I figured you would be doing something like that	by etwas_egal	2007-04-30 14:54:51
Well, as you can imagine, my matrices are dense	by shadowboy813	2007-04-30 16:55:25
Very dense--but I am dealing with a dimension-reducing approximation. My vector is the configurational space of the protein, but instead of it being a 1700-something vector, I can look at only the alpha carbons (which reduces the particle count to 1 per amino acid--plus it's a valid approximation since the side-chains are going to flop around much more than the alpha carbons anyway. I'm just worried that due to the stability of alpha carbon positions (this is an equilibrium simulation) the clusters will be so close together that there won't be any clear distinction between them. Right now I am working on opening the binary trajectory file directly rather than using VMD's tcl interface to do the cluster analysis (which would be slow and cumbersome I'd assume). I've never needed to directly read a binary trajectory file until now.
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