[gmx-users] center of mass removal
burisch at bph.rub.de
Wed Dec 26 07:52:41 CET 2007
Li Qiang schrieb:
> Dear all,
> 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"
> 2, Can anybody tell how the COM removal is achieved (in gromacs or other
> methods available)?
> thank you
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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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