[gmx-developers] Question on SHAKE equations

"Pablo García Risueño" Risueno at physik.hu-berlin.de
Mon Jun 10 10:57:37 CEST 2013

Thank you very much for the answer. It is said that:

"A practical issue is that not many people use shake, since LINCS works in
parallel too."

But I thought that SHAKE was used when bond angles are constrained, this
is when bond lengths of heavy atoms are constrained (since bond lengths of
heavy atoms and bond angles of hydrogen have the same period). Isn't this
correct?

Thank you very much

> On 2013-06-07 19:26, "Pablo García Risueño" wrote:
>> 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, and the equation (5.6) of the SHAKE paper
>> (see 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:
>>
>> SHAKE var               Gromacs var
>>                            omega=1
>> d^2 - (r')^2               diff
>> 1/(2(1/m_i+1/mj))          m2[ll]
>> \vec{r}_{ij}\cdot\vec{r}'_{ij}  rrpr
>> g                         lagr[ll]
>>
>> being ll the constraint index. However, I think that the term
>> proportional
>> to g^2 in the equation (5.6) of SHAKE paper is not in the Gromacs code.
>> This term is relatively small, but I was assuming that it is not
>> negligible. Could some developer explain me whether this term is
>> neglected, or it is included in the calculations elsewhere?
>>
>
> I don't have the complete overview, so I will assume your observation is
> correct.
> Since the algorithm is iterative the second term may not be needed,
> although it might be converge in fewer iterations with it.
>
> A practical issue is that not many people use shake, since LINCS works
> in parallel too.
>
>> Thank you very much. Best regards
>>
>>
>>
>> --
>>
>> 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
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
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--

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