[gmx-users] number of index elements not multiple of 3, these can not be angle triplet

[Justin A. Lemkul]

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.amit at gmail.com 
> <mailto:kgp.amit at gmail.com>> wrote:
> 
>     try the -type option with dihedral
> 
>     amit
> 
>     On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous <carlajamous at gmail.com
>     <mailto:carlajamous at 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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