Hi again,
this is the COM velocity of the peptide only? Then these peaks are
perhaps a PBC artifact?!
Actually I never saw such a fast movement in my runs so far that the
solute was speeding through the box over and over. But perhaps the
velocity is so high in your case that one has to take care about that,
to prevent a flying ice cube. But as I said, removing just the solutes
COM velocity may create artifacts IMHO, too.
Perhaps one of the COM removal experts can comment here?! ;-)
Merry Xmas
C.
Li Qiang schrieb:
> hi Christian,
>
> Thanks for the reply. I have plotted the the rate of center of mass
> motion and found there are peaks with certain time interval. I think
> that is not only a visual problem but like fly ice cube problem(not
> sure). As a comparison, when a large protein is simulated, the
> rate(velocity) of COM is "constant".
>
> Yes. the default way GROMACS do is system COM removal at each step.
>
>
> how does the program remove this center of mass motion?
>
> Merry Xmas
>
> Qiang
>
> On Wed, 2007-12-26 at 14:52 +0800, Christian Burisch wrote:
>> Li Qiang schrieb:
>>> Dear all,
>> Hi Qiang,
>>
>>> I am simulating short peptide in GROMACS. Center of mass need to be
>>> removed to keep the peptide from jumping out.
>> I guess this is only a visual problem, but read page 18 in the manual.
>>
>>> I have two questions about this:
>>> 1, when I remove COM of the peptide using comm_grps, do I need to put
>>> the solvent(including the counter ion) at the same time for COM removal?
>> In a solvent simulation I would do linear COM removal of the whole
>> system only (as is done automatically). I guess there will be
>> artifacts if you just remove the translation of the solute (slight
>> collisions with the solvent on one side and underpressure on the other
>> side). But anyone please correct me if there is a clever algorithm to
>> prevent that! ;-)
>>
>>> or the program will take care of the whole system automatically?
>> Gromacs does COM removal automatically ("linear" on a group called
>> "rest", which means the whole system if no comm_grps is given, as
>> written in the log file) if you don't explicitly turn it off ("none"
>> or nstcomm=0).
>>
>> Merry Xmas
>>
>> Christian
>>
>>
>>> 2, Can anybody tell how the COM removal is achieved (in gromacs or other
>>> methods available)?
>>>
>>> thank you
>>>
>>> Qiang
>>>
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--
Dr. Christian Burisch
Protein Mechanics and Evolution Group
CAS-MPG Partner Institute for Computational Biology
Shanghai Institutes for Biological Sciences
320 Yue Yang Road, 200031 Shanghai, P. R. China
Tel: +86 21 54920478 Fax: +86 21 54920451
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