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

[Arneh Babakhani]

ok.  I'll give it a shot too, should get the same answer , will be a 
good way to double check,

Arneh

Alan Dodd wrote:
> 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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