[gmx-developers] Question on SHAKE equations

"Pablo García Risueño" Risueno at physik.hu-berlin.de
Fri Jun 7 19:14:39 CEST 2013

Dear Gromacs developers

I am studying the Gromacs implementation of the SHAKE algorithm. As far as
I know, it corresponds to the cshake procedure, which lies in the shakef.c
file. The equation (5.6) of the SHAKE paper
(http://www.sciencedirect.com/science/article/pii/0021999177900985) is
essentially in

acor = omega*diff*m2[ll]/rrpr
lagr[ll] += acor;

where the relationship between variables is:

 omega=1, diff


Dr. Pablo García Risueño

Institut für Physik und IRIS Adlershof, Humboldt Universität zu Berlin,
Zum Grossen Windkanal 6, 12489 Berlin, Germany

Tel. +49 030 209366369

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