two independent groups of constraints

From: Marcin Krol (
Date: Thu Apr 30 2009 - 07:44:41 CDT


I'd like to perform a simulation of an extended polypeptide chain where
I restrain one end of the chain in 2D (say y,z and it can still move
along x axis) and I have rotating constraints of the other end (in y,z
plane). Basically, I want to be able to rotate one end of the chain,
while the other end is prevented from rotating, but can move so that the
chain can elongate or shorten.
Ideally, I could do it if I could define two independent groups of
constraints. Is it possible in namd?
The other way is to use constraints + TMD, but this is much more
complicated (need to generate temporary target structures).

Thanks in advance

Dr Marcin Krol
Zaklad Bioinformatyki i Telemedycyny
Collegium Medicum Uniwersytet Jagiellonski

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