[gmx-users] Re: gmx-users Digest, Vol 28, Issue 42

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 14 19:24:52 CEST 2006

Eudes Fileti wrote:
> Dear David
> Actually I posted my doubt in Vol 28, Issue 38. There I detailed more. 

sorry, I don't memorize it all...

> Anyway, my system is 1 C60 molecule in 1000 ethanol molecules. As said, 
> I need of structures that do not remember the previous one, i.e. that 
> are structural and statistically not correlated.
> For this, up to now, I have attemped to use the autocorrelation function 
> of the energy and the block averaging process, but I am still uncertain 
> about the results.
> An interesting option it could be the analyzis of van Hove function, but 
> I dont kwow how calculate them.

You probably want to know a characteristic interaction time between the 
C60 and ethanol. Since this will be dominated by Van der Waals 
interactions you can try to compute the autocorrelation time of C60 - 
Ethanol-Carbon contacts (using the CVS version of g_hbond) and then
use something on that order of time.

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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