Generalized solvent boundary potential or similar tricks for huge systems in NAMD??

From: Jacob Poehlsgaard (
Date: Thu Nov 30 2006 - 03:15:35 CST

Dear all

  I'm trying to run some simulations on local changes inside the
ribosome. As this is a huge structure, I have to make some effort to cut
down on CPU time. Reading some older papers I came across something
called "Generalized solvent boundary potential", which is apparently
supported by CHARMM.

  As I understand it, the idea is that you define a bubble inside a
macromolecule that you want to look at. Outside a certain radius
defining the bubble, the larger part of the macromolecule and the
solvent is reduced to an implict energy function of some kind, allowing
for long range interactions from distant parts of the macromolecule to
influence the region of interest. This should be very cheap on CPU time.

  I have a feeling that this might be possible in NAMD using TCL
boundary forces, but I have no idea how to get started with this.

  Any help or thoughts would be appreciated!

Jacob Pøhlsgaard
PhD student, SDU, Denmark

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