[gmx-users] calculation of angle between two groups

Justin Lemkul jalemkul at vt.edu
Thu Jul 26 15:51:34 CEST 2012

On 7/26/12 9:48 AM, niaz poorgholami wrote:
> Dear Mark
> thank you for your concern.when I tried the g_sgangle program
> it gave me
> Fatal error:
> Something wrong with contents of index file.
> the index file was the one I used during the simulation and I made that
> with this command:
> make_ndx -f em.gro -o index.ndx
> and the groups for temperature couplig was
>   tc-grps		= MOL_LIG Water_and_ions
> it means that I coupled carbon nanotube(MOL) and surfacatnt(LIG) together.
> I would be really pleased if you could help me.

The help information from g_sgangle -h (or the manual) should give you some 
clues.  The index groups chosen must be a multiple of 2 or 3 in size, given the 
normal groups that are analyzed (water, with 3 atoms).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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