[gmx-users] Regarding calculation of angles

[Justin Lemkul]

On 4/9/17 12:27 PM, Dilip H N wrote:
> Suppose for eg., in glycine how can i calculate the angle between nitrogen
> and hydrogen attached to it, angle between C alpha and H alpha etc.,
>

You can't calculate the angle between two angles; you need at least three.

Regardless, you can easily just write these index groups by yourself in a text 
editor when you have identified suitable atom triplets of interest.

-Justin

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> On Sun, Apr 9, 2017 at 9:49 PM, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
>
>> Hello,
>> I have ran a amino acid simulation, and i want to calculate the angle
>> between the atoms in amino acid molecule. how can i calculate it..??
>>
>> gmx angle [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-od [<.xvg>]]......
>>
>> 1] here what index does it refer to .?? is it similar to the the RDF
>> indexing ..??
>>
>> 2] how can i make these indexes...??
>>
>> Thank you
>> --
>> With Best Regards,
>>
>> DILIP.H.N
>> Ph.D Student
>>
>>
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>>
>
>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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