[gmx-users] Regarding calculation of angles
jalemkul at vt.edu
Mon Apr 10 00:49:00 CEST 2017
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.
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> On Sun, Apr 9, 2017 at 9:49 PM, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
>> 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,
>> Ph.D Student
>> <https://mailtrack.io/> Sent with Mailtrack
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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