Applying conformational constraints during simulation

From: poker_at_physics.usyd.edu.au
Date: Mon Oct 22 2007 - 22:08:46 CDT

I have a protein which I am pulling from a binding site by SMD (center of
mass coordinates). In order to keep the protein properly folded I am
planning on applying a coordinate-based constraint based on aligning its
backbone reference to the protein's current position in the system.
Is this possible in NAMD? There's an equivalent process in the latest
CHARMM (recorded in cons.doc under RMSD constraints) - is there a way to
align a reference set of coordinates during the simulation?

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Also, is it possible to freeze the coordinates of the ligand and still move
it during simulation?
Poker.
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