[gmx-users] which tool to use a measure a user-defined angle in a traj

[Alan Dodd]

Fair enough, but I'll just repeat that g_bundle does *exactly* what you want in your example - provide it with an index file with two groups with the COMs defining the ends of the axes (in your case, one C in one group and one O in the other) and the option -z, and it'll dump out a file of the angle those axes make with the z-axis.  Don't be put off by the way it appears to be designed for helices.

----- Original Message ----
From: Arneh Babakhani <ababakha at mccammon.ucsd.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, July 17, 2007 1:30:22 AM
Subject: Re: [gmx-users] which tool to use a measure a user-defined angle in a traj


ok, thanks.  I like Chris's suggestion.  I'll try using matlab to parse 
it out (b/c matlab can easily ingest column formatted data),

Arneh

Tsjerk Wassenaar wrote:
> Hi Arneh,
>
> I think you're out of luck here. However, this is an excellent
> exercise to get started with writing custom made analysis tools :)
> Alternatively, you could output the coordinates for the C and O using
> g_traj and use a script to calculate the angles with the z-axis, in
> case it's a single bond you're interested in.
>
> Cheers,
>
> Tsjerk
>
> On 7/13/07, Arneh Babakhani <ababakha at mccammon.ucsd.edu> wrote:
>> Hi,
>>
>> Looking through the gmx tools . . . was wondering, which tool would one
>> use (if such a tool exists) to measure the fluctuation of a user-defined
>> angle in a trajectory.
>>
>> For instance, I want to measure the angle defined by a carbonyl vector
>> (a vector going through a C=O bond) in my molecule and the z-axis of the
>> simulation box.  How do I define this angle, and which tool would I use
>> to measure it in each frame of my trr?
>>
>> Thanks,
>>
>> Arneh
>>
>>
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