[gmx-developers] Question on SHAKE equations
Berk Hess
hess at kth.se
Mon Jun 10 14:51:38 CEST 2013
On 6/10/13 14:20 , "Pablo García Risueño" wrote:
> Dear Berk
>
> I am a bit concerned about this point. Let us restrict ourselves to the
> case of all H bond angles constrained. I was assuming that every H had one
> single (arbitrary) constrained bond angle. This is, in the scheme below,
> e.g. the angle C1-C2-H would be constrained, but not the H-C2-C3 angle.
> Isn't this true?
No, that's arbitrary and asymmetric.
>
> H
> |
> C1--C2--C3
>
> In some literature I read that the vibration period of H bond angles is
> the same as that of heavy atoms bond lengths (the Gromacs option h-angles
> for constraints seems to assume this). Isn't this Gromacs option
> proceeding as stated above?
>
> Can you give me some reference where the procedure of 'virtual sites' to
> constrain H bond angles is explained?
Search in the Gromacs manual. The reference is also in there.
Cheers,
Berk
>
> Thank you very much. Best regards
>
>
>> On 6/10/13 12:15 , David van der Spoel wrote:
>>> 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.
>> But note that constraining all-angles will lead to incompatible
>> constraints, unless the molecule is very small.
>> Constraining all angles involving hydrogens has similar issues. We use
>> virtual sites to remove H-angle vibrations.
>> So in practice the only molecule for which angle constraints are used is
>> water, but there SETTLE is algorithm of choice.
>>
>> Cheers,
>>
>> Berk
>>>> 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
>>>>> --
>>>>> gmx-developers mailing list
>>>>> gmx-developers at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-developers-request at gromacs.org.
>>>>>
>>>>
>>>> --
>>>>
>>>> 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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>>
>
> --
>
> 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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