[gmx-users] Re: gmx-users Digest, Vol 81, Issue 204

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jan 29 08:52:36 CET 2011

On 29/01/2011 6:32 PM, Thomas Koller wrote:
> Hello!
> Due to the fact that I still got no reply I ask you once more:

Check out the advice here http://www.gromacs.org/Support

> i) I studied the topic of autocorrelation function in Gromacs. For instance, I can define any distance between different atoms of my molecule over time (g_dist) as *.xvg file. For g_analyze, I use this as input and plot the autocorrelation function (-av) and can fit it with -fitfn exp. But when I want to use the Legendre option -P 2 to get a second order legendre polynomial (which is used quite often in literature) the error appears:
> Incompatible mode bits: normal and vector (or Legendre)

Probably nobody can help unless they know your command line.

> I think that I need vectors but this can not be done in Gromacs, does it?. How can I get Legendre functions, also for dihedrals?
> ii) I use bond type 1 (harmonic bond potential), but I get always linear spiky bond distribution functions, no Gaussian distribution. What is the problem?

Nobody can help unless they know what you've done and what the output 
looks like. That might mean uploading a graphic of your plot file to 
some free web hosting service and providing links.


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