[gmx-users] g_velacc again

[David]

On Thu, 2003-08-28 at 23:02, Nuno R. L. Ferreira wrote:
> Dear all gmx users
> Can anibody give me some help on this? My aim is to obtain the diffusion
> coefficient for a peptide. Since that for calculating MSD's of proteins with
> need longer simulations, and the statisticall error with just one molecule
> is "big" (MSD vs time does not show a good straight line), I was thinking in
> VACF vs time. But till now I did not understood how to calculate Dt from the
> information of g_velacc calculation. Where is the integral of VACF? Am I
> missing something?
> 
> Many thanks,
> Nuno
> 
> P.S. I apologise if my explanation is a bit confuse.
> 
> 
Have you looked at the graph in xmgrace? It is probably easiest to start
there, use the integration function to see how ill-behaved the ACF is.
It may just fluctuate wildly. Then use the non-linear fit to fit your
ACF to a function of your choosing and integrate again. You can probably
get the same result from gromacs if you use some more flags like
-beginfit and -endfit

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> #######
> Nuno Ricardo Santos Loureiro da Silva Ferreira
> Grupo de Química Biológica
> Departamento de Química
> Faculdade de Ciências e Tecnologia
> Universidade de Coimbra
> 3004-535 Coimbra
> Portugal
> 
> Phone: +351 239 852080
> Fax: +351 239 827703
> www.biolchem.qui.uc.pt
> ####
> 
> 
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-- 
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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