[gmx-users] angle

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello,
> I am doing solvation of glucose. I am trying to calculate a angle between
> three selected carbon atoms.
> If I run g_angle using angle.ndx file it consider all carbon atom. In
> force field C-C-C 112.5 is specified so it’s making a group of all carbon
> atoms. I am interested in selected carbon atoms.
> How can I plot an angle of selected three carbon atoms?

Make an appropriate index group, which it doesn't sound like you've done.  If 
there's a specific angle you want to measure, you don't even necessarily need 
make_ndx, just write the group using a text editor with the appropriate atom 
numbers.

-Justin

> 
> Thanks
> 
> Nilesh
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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