[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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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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