Re: two independent groups of constraints

From: Eduardo Cruz-Chu (chucruz_at_ks.uiuc.edu)
Date: Thu Apr 30 2009 - 13:54:18 CDT

The setup sounds complicated, but sure, you can do anything
using tcl forces. tcl-forces and tclBC forces allow you to add any kind of
force to your system, as long as you can defined as a tcl command.

You can start reading the user-defined forces tutorial.

http://www.ks.uiuc.edu/Training/Tutorials/science/forces/forces-tutorial-html/

For basic tcl scripting, you can take a look at the vmd-tutorial.

Regards.

Eduardo

On Thu, 30 Apr 2009, 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?
> 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
>
> --
> Dr Marcin Krol
> Zaklad Bioinformatyki i Telemedycyny
> Collegium Medicum Uniwersytet Jagiellonski
> e-mail: mykrol_at_cyf-kr.edu.pl
>

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