[gmx-users] angle calculation

[Adamu, Aliyu]

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

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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