Tutorial-l Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Oct 26 2007 - 11:18:21 CDT

Those are the coordinates of the first nitrogen of deca-alanine. If
you look at the pdb, you'll notice it's only approximately 0
(actually, 0.166 0.267 -0.304) but for the purposes of the
tutorial, it's close enough.

On Oct 26, 2007, at 5:38 AM, Per Jr. Greisen wrote:

> Hi,
>
> I have a question to the tutorial on stretching alanine - in the
> smd.tcl, the constraints are set to zero
>
> set c1x 0.0
> set c1y 0.0
> set c1z 0.0
>
> which are latter used in the method proc calcforces to determine
> the forces on each atom. How are these constraints determined?
>
> Any advice or help appreciated. Thanks in advance
>
> Best regards
> Per Jr. Greisen
>

**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**