[gmx-developers] shake stuff

Mark Abraham mark.j.abraham at gmail.com
Tue Apr 5 14:49:59 CEST 2016


Please don't reply to digests if you want to engage in discussion :-)

On Tue, Apr 5, 2016 at 2:12 PM Carl Christian Kjelgaard Mikkelsen <
spock at cs.umu.se> wrote:

> Hello,
> Thank you very much for confirming that I have identified the exact
> constraint functions used by cshake().
> Would you please consider the second part of my conjecture and confirm if
> I have the correct vector equation as well? Again, even the smallest
> detail, such as the exact scaling of the Lagrange multiplier is critical.
> As I stated in my first email, I believe that cshake() is solving the non
> linear vector equation
> g(rprime - inv(M)*Dg(r)*lambda) = 0
> where
> rprime is the unconstrained atomic coordinates for the next time step
> r      is the constrained atomic coordinates at at current time step
> M      is the diagonal mass matrix
> lambda is a Lagrange multiplier
> cshake return both the new constrained atomic coordinates rnew given by
> rnew:=rprime - inv(M)*Dg(r)*lambda
> and the vector lambda itself.
> I am afraid that the comment in cshake() which you refer to has been a
> source of confusion for me. In particular, there is no Greek letter eta
> used on page 336 of the original SHAKE paper.

Sorry, literacy problem here. I meant gamma when I wrote those docs.

> Moreover, I have not been able to find any evidence of any division with
> the constraint distance.

You shouldn't expect to see a transliteration of the algebra, because this
is floating-point computation and division should be routinely avoided. But
you should expect to see something equivalent in the code that refers to


> Kind regards
> Carl Christian
> --
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