From: Jacob Pøhlsgaard (jacobp_at_bmb.sdu.dk)
Date: Tue Apr 18 2006 - 04:39:20 CDT
I'm looking to simulate a very small area of a very large complex.For this I'm going to freeze some residues, restrain others and allow the atoms in the area of interest to move freely.
My question is if anyone knows how much computational cost I have to pay by including the whole (~150.000 atoms) complex as frozen atoms? Is there some general rule of thumb?
Is it a good idea to include all the residues at all? I'll have atoms way beyond the electrostatic cutoff, but as I understand it, there's still a a contribution to electrostatics that far away since I'm using the PME method.
Department of Biochemistry and Molecular Biology
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