[gmx-users] computing dihedral given 4 atoms

[sandeep somani]

ok, just realized that -ov option of g_angle gives the values for each
frame.

ignore my previous mail.

Rgds
Sandeep


On Sat, Sep 26, 2009 at 6:32 PM, sandeep somani <ssomani at gmail.com> wrote:

> 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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