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 <ssom...@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 <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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