[gmx-developers] Question on SHAKE equations

[David van der Spoel]

On 2013-06-10 10:57, "Pablo García Risueño" wrote:
> 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?
>
That's up to the user, but LINCS can be used too for angles when the 
number of iterations is increased a bit (although not too many people 
use angle constraints either). Nevertheless gromacs supports the shake 
algorithm and hence it should work.
> 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.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> --
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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
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se