[gmx-users] angle calculation

[Justin Lemkul]

On 7/20/16 12:17 PM, Adamu, Aliyu wrote:
> Hello Justin,
>
> Thanks a lot for your email. but I have no suitable vectors available in my
> .ndx file and I have no idea on how to write the simple script you suggested.

Your index file won't contain vectors, it contains groups of atoms.  Those 
groups of atoms can be used to define vectors between them using selection 
syntax available in many GROMACS tools.  Please have a look at the gmx gangle 
help description for how to select them and "gmx help selections" for learning 
how to use the syntax.  I have not tried to do this exact calculation but it 
should be possible if properly specified.  If you have further questions about 
this, please post exactly what you have tried, what it returned (wrong result, 
error, etc) and we can advise further.

> Please can you please elaborate or give a template of the script?
>

It's very simple.  One can easily calculate the vector between two points.  The 
angle between those vectors is obtained with simple mathematics.  Any scripting 
language like Python or Perl can be used to parse the file.  I strongly 
recommend learning at least one programming/scripting language for anyone in the 
field of computational chemistry.  If all the tools you need aren't available 
already, you'll have to create your own!

-Justin

> Many thanks Aliyu Adamu ________________________________________ From:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin
> Lemkul [jalemkul at vt.edu] Sent: Wednesday, July 20, 2016 1:40 PM To:
> gmx-users at gromacs.org Subject: Re: [gmx-users] angle calculation
>
> On 7/20/16 3:58 AM, Adamu, Aliyu wrote:
>> Hello all,
>>
>> I am interested in calculating angle between 3 specific groups. Is it
>> possible to generate the angle.ndx file for theses specific groups in
>> GROMACS 4.6.7? If yes, please how? And if no is there any option?
>>
>> Please can any one help
>>
>
> gmx gangle with suitable vector selections may work, otherwise output the
> COM coordinates of the three groups (gmx traj -ox -com) and write a simple
> script to calculate the angle between those vectors.
>
> -Justin
>
> -- ==================================================
>
> 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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-- 
==================================================

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

==================================================