[gmx-users] 3-site methanol model (Re: C. Freudenberger)

David spoel at xray.bmc.uu.se
Thu May 22 19:05:01 CEST 2003

On Thu, 2003-05-22 at 16:55, Christoph Freudenberger wrote:
> > 2) When performing methanol Dt calculations around the peptide, what is the
> > best way to do this ? I mean, should I fixe the peptide all along the MD, or
> > let it translate?
> Personally I would avoid any artifical influences on the system if there is
> no actual need to do so. Hence I would not use any contraints or freeze groups.
> But being an organic Chemist my molecules are way smaller.
> BTW... I'm just wondering what happens in a protein box simulated with comm...
> I figure as a large part of the systems mass belongs to the protein, the
> protein might propably not diffuse at all... Is that correct?

No it will diffuse as it should with roughly the right Diffusion
constant (within a factor of two).

  author = 	 {P. E. Smith and W. F. van Gunsteren},
  title = 	 {Translational and Rotational Diffusion of Proteins},
  journal = 	 {J. Mol. Biol.}
  year = 	 1994,
  volume =	 236,
  pages =	 {629-636}

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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