[gmx-users] angle

[Oliver Grant]

You could load your gro and trr file into vmd, label the angle, save the
file and plot using excel.

Oly

On 28 April 2010 22:26, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>
>>
>>
> --
> ========================================
>
> 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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