[gmx-users] g_velacc

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 4 07:53:12 CEST 2013

On 2013-07-04 05:38, Ishwor wrote:
> Dear all
> I  have calculated the diffusion coefficient using command g_msd and I want
> to calculate diffusion coefficient using command g_velacc. I am confused
> with some terms.
> 1>I have looked the manual page of g_velacc and i found the statement "the
> time interval between data collection points is much shorter than the time
> scale of the autocorrelation." What actually does that mean?
> 2>I am also confused with the flag -acflen ( I have found that it describes
> the number of frames to be taken into consideration.Does that mean I have to
> take the points ,to integrate,  in such a way that it matches with the time
> i have used in g_msd for fitting of Einsteins equation)
> 3> what does the flag -nonormalize indicates. Do I need to use it
> necessarily?
> 4>Is the  command "g_analyze -f *.xvg -integrate" sufficient for
> integration?
> Ishwor

Lots of good questions.
Have you actually tried?

You need to store the Velcoties quite often, maybe every 20 fs 
(depending on the system).
> Nepal
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

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

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