[gmx-users] angle

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 28 23:26:04 CEST 2010

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 


> Thanks
> Nilesh


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


More information about the gromacs.org_gmx-users mailing list