[gmx-users] g_bundle issue

[Thomas Piggot]

Have you tried using the -z option to calculate the angle with respect 
to to the z axis? I vaguely remember having an issue like this a few 
years ago and this fixed the problem, sorry I can't be more specific.

Cheers

Tom

Anirban Ghosh wrote:
> 
> Hi ALL,
> 
> I tried to calculate the helix tilt of a single helix (TM5) among 7 
> helices using g_bundle. In the index file I defined the two groups (top 
> & bottom) as the C-alpha of the first 5 and last 5 residues of TM5 
> respectively. But in the bun_tilt.xvg file I am getting the values as:
> 
> ---------------------------------------------------------------------------------------------------------------------------------------
> # This file was created Thu May 20 15:29:50 2010
> # by the following command:
> # g_bundle -f prot.xtc -s prot.tpr -n TM5_top_bot.ndx -na 1
> #
> # g_bundle is part of G R O M A C S:
> #
> # GRowing Old MAkes el Chrono Sweat
> #
> @    title "Axis tilts"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "(degrees)"
> @TYPE xy
>           0      0
>           2 0.0197823
>           4      0
>           6 0.0197823
>           8      0
>          10      0
>          12 0.0197823
>          14      0
>          16 0.0197823
>          18      0
>          20 0.0279765
>          22      0
>          24      0
>          26 0.0197823
>          28      0
>          30      0
>          32      0
>          34      0
>          36      0
>          38 0.0197823
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> And when plotted it gives a blank plot. Why it is coming like this? Am I 
> doing anything wrong? Any suggestion is welcome.
> The contents of the index file is:
> 
> [ top ]
> 1844 1850 1858 1866 1878 1896 1904 1913 1922 1940 1948 1956 1965 1974 1983
> 1991
> [ bottom ]
> 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132
> 2138 2146
> 
> 
> Regards,
> 
> Anirban
> 

-- 
Dr Thomas Piggot
University of Southampton, UK.