[gmx-users] g_velacc
David van der Spoel
spoel at xray.bmc.uu.se
Sat Aug 30 10:56:19 CEST 2008
rams rams wrote:
> Dear Users,
>
> I am trying to calculate the velocity correlation functions to estimate
> the diffusion constant of my protein which is having nearly 50 residues.
> I am using the following command:
>
> g_velacc -f .trr -s .tpr -n .ndx -o .xvg -fitfn exp
>
> the output is the following:
>
> COR:
> COR: Correlation time (plain integral from 0.000 to 2500.000 ps) =
> 0.90300 ps
> COR: Relaxation times are computed as fit to an exponential:
> COR: y = exp(-x/a1)
> COR: Fit to correlation function from 0.000 ps to 2500.000 ps, results in a
> COR: Fit from Integral Tail Value Sum (ps) a1
> (ps)
> COR: 0.0000e+00 0.0000e+00 1.0458e-01 1.0458e-01 1.0458e-01
>
> I have no idea about the output to understand. I understood it is trying
> to fit to the equation it displayed but have no idea about the number
> 0.90300 ps.
>
> The .xvg plot I got is so surprising its just a straight line parallel
> to time axis. I am sure I am making some mistake as I am using g_velacc
> for the first time.
Have you zoomed in to the area close to t=0? It ssems from the integal
that your ACF is pretty short. What kind of system is this?
To compute a diffusion constant you don't need the expfit.
>
> From this if we want to get the Diffusion coefficient we need to
> integrate the correlation time from 0 to infinitive as it is described
> in the manual. Is there any way we can do it by using any of the options
> or we need to do it separately by using any other tools ? If so please
> let me know.
>
> I also wanted to know the following things:
>
> What does the following options do:
>
> -normalize
> -integrate (in g_analyze)
>
> -fitfn (there are couple of options are given if any one have idea about
> the sources for them ?)
>
> I calculated the diffusion coefficients using g_msd also, it gave the
> diffusion coefficient value as 6.0*10^-6. Which is quite large compared
> to the values reported in the literature which are around 2.0*10^-6.
> Whats going wrong here also it is not generating the output .xvg file.
> (It is complaining input/output fatal error).
>
> Thanks in advance,
> Ram.
>
>
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>
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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