[gmx-users] Distance for contacts of 0.6 nm

[David van der Spoel]

On 2010-03-17 19.24, Stefan Hoorman wrote:
> I´ve searched the manual but could not find the reference for the cutoff
> distance used to analyze contacts in several tools of gromacs. Gromacs
> usually uses 0.6 nm in order analyze contacts between atoms. If
> possible, I would like to know where that information was published.
> Thank you
>
You can set the cut-off to whatever you like. This kind of analyses 
allways carry a certain amount of randomness. In the best case you 
should show that your results are not dependent on this kind of choices. 
We are working on different algorithms that avoid this kind of cut-offs, 
by e.g. using autocorrelation functions.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se