[gmx-users] end to end normalized vector

[Smith, Micholas D.]

I guess my question is angle relative to what? If you are talking about comparing end to end vectors between molecules groups like:

Nterm1---------->Cterm1 (group 1)

Cterm2<---------Nterm2 (group 2)

You could make an index file with one group being A1 and B1 and other being A2 and B2, and use g_angle (or gmx angle in the newest version) to compute the angles between these two vectors.

If you are talking one protein, you could do something like

Nterm-------->median-residue--------->Cterm

Where you define your vectors to go from the median residue to the Nterm and from the median residue to the Cterm.


===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of pratibha kapoor <kapoorpratibha7 at gmail.com>
Sent: Thursday, April 23, 2015 7:06 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] end to end normalized vector

Hi,
I would like to calculate angle between normalized end to end vectors. How
can this be done in gromacs? Although end to end distance can be computed
using g_dist but this contains no information about direction.

Thanks
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