Carla Jamous wrote:
Thank you,

It worked, one last question. Something is not very clear to me:

-ov: plots the average angle of a group of angles as a function of time!! What does it mean?

Because I'm getting positive and negative values in the same plot. Are these values the values of my dihedral angle as a function of time?


The -ov option gives the average angle of all angles contained in the index group over time. If your selected group contains only one angle, then the average at any given time is equal to the instantaneous value at that time.

-Justin

Thanks again,
Carla

On Fri, Jan 7, 2011 at 11:30 AM, Amit Choubey <kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>> wrote:

    try the -type option with dihedral

    amit

    On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous <carlajam...@gmail.com
    <mailto:carlajam...@gmail.com>> wrote:

        Hi Everyone,

        Please I'm trying to calculate one dihedral angle as a function
        of time during my simulation.
        For this, I used g_angle. In the manual (version 4.0.3) it says:
        the indexfile should contain atom-triplets or atom-quadruplets
        for dihedrals.

        I put an atom-quadruplet in my index file, but when I run
        g_angle -f .xtc -n .ndx -od .xvg

        and I select the group of atom-quadruplets, gromacs crashes and
        shows this error message:
        number of index elements not multiple of 3, these can not be
        angle triplets

        So actually g_angle only calculates angles not dihedrals?

        Thanks

        Carla


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--
========================================

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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