Re: Colvars: Using "Alpha" Component

From: Giacomo Fiorin (
Date: Fri Sep 24 2010 - 16:35:44 CDT

Ouch, that sounds like a bug... The alpha component is kind of special, in
the sense that unlike the others it looks up its atoms automatically, and I
believe that one of our recent changes could interfere with it.

Are you using a precompiled binary or did you compile NAMD on your own? If
so, as a quick fix I can tell you how to strip out those recent changes and
make alpha functional again.


---- ----
  Dr. Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
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On Fri, Sep 24, 2010 at 5:10 PM, Alexander Predeus <>wrote:

> Giacomo,
> the strange thing is that there's no such keyword. My whole colvar
> input is in the original email. I just wanted to test folding and
> unfolding of alpha-helix under a harmonic restrain in my system. Any
> idea why is this happening?

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