Re: two independent groups of constraints

From: Axel Kohlmeyer (
Date: Thu Apr 30 2009 - 08:14:01 CDT

On Thu, 2009-04-30 at 14:44 +0200, Marcin Krol wrote:
> Hello,


> 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?

this sounds like a job for TclForces. this way you can add forces
to atoms any which way you like.


> The other way is to use constraints + TMD, but this is much more
> complicated (need to generate temporary target structures).
> Thanks in advance
> Best
> Marcin

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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