[gmx-users] Simulation single unit of a dimer

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 6 09:12:32 CET 2006

raja wrote:
> Dear gmxions,
> The protein, which I am going to simulate, is a dimer, but my study
> through MD is not related of dimer interaction but its catalytic
> activity. So my question is can I simulate a unit of the dimer? Will
> that system be physically right to simulate? The individual unit of the
> dimer is performing the same catalytic activity but act individually.
> Your thought for this question would be very useful for me.
> With thanks!
> B.Nataraj
It depends, the dimer may give stability that is necessary for 
catalysis. To be on the safe side use the dimer. It will also give you 
twice the statistics for your analysis. If you'd use the monomer a 
referee will ask you whether that is justified as well.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se

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