[gmx-users] computing dihedral given 4 atoms

[sandeep somani]

Hi Justin

I had missed the -type flag of g_angle.

But it gives the distribution of the dihedral, not the value corresponding
to each frame. for example,

 g_angle_d -f mol.xtc -n torsion.ndx -type dihedral
followed by selection of a group with 4 atoms generated one output file
angdist.xvg which looks like

@ title "Dihedral Distribution: Phi=180.0_2_43.93"
@ xaxis label "Degrees"
@ yaxis label ""
@TYPE xy
@ subtitle "average angle: 0.445455\So\N"
@with g0
@ world xmin -180
@ world xmax 180
@ world ymin 0
@ world ymax 0.0409091
@ xaxis tick major 60
@ xaxis tick minor 30
@ yaxis tick major 0.005
@ yaxis tick minor 0.0025
-180 0.035465
-179 0.032967
  :
  :


I guess it should be easy to modify the code to get the value out for each
frame.

Thanks
Sandeep






On Sat, Sep 26, 2009 at 5:54 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> sandeep somani wrote:
>
>> hi
>> I have simulated a molecule (not a standard protein) with gmx and now need
>> to compute dihedral angles between specified atoms for all frames of in the
>> .xtc file.
>> Is there any utility along the lines of g_bond whcih computes the
>> dihedral/torsion angle given 4 atom numbers in a index file group ?
>>
>
> g_angle -type dihedral
>
> -Justin
>
>  Based on the manual, g_chi and g_dih come close but do not exactly fit the
>> bill. Any work around ?
>> Thanks Sandeep
>> --
>> Graduate Student Chemical Physics
>> Univ of Maryland College Park
>>
>>
>>
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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