[gmx-users] center of mass removal
liqiang at bii.a-star.edu.sg
Wed Dec 26 08:16:16 CET 2007
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?
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
> > 2, Can anybody tell how the COM removal is achieved (in gromacs or other
> > methods available)?
> > thank you
> > Qiang
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