constraining distance

From: Anahita Tafvizi (
Date: Wed Oct 04 2006 - 13:16:29 CDT

Dear All,

I wonder if there is a way to constrain the distance in NAMD, I know there
are ways to constrain the positions, but is there any ways for distance?

In my simulation a protein is moving along DNA, and I don't want my protein
to become unfold due to the force, so I want to constrain the distance
between CA atoms such that the protein will behave almost as a hard object.

Does anyone know any tools in NAMD?

I appreciate any suggestion.

Anahita Tafvizi
PhD Candidate
Physics Department
Harvard University
17 Oxford Street
Cambridge, MA 02138

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