restrain ligand in z-interval

From: Magnus Andersson (magnus.andersson_at_scilifelab.se)
Date: Mon Apr 15 2013 - 06:37:26 CDT

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Hi all,

I have docked a ligand into a membrane protein and want to simulate the system with the ligand exploring the inside of the protein, but not leave into the bulk solution.

selectConstraints can be used to keep a ligand at a certain z-coordinate.

But, I need to define a window in the z-dimension, rather than a single point.

Can this be done with NAMD?

Cheers /

Magnus Andersson

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