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 <jalem...@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 >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > 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 > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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