[gmx-users] end to end normalized vector

[Erik Marklund]

Hi,

I suggest running g_traj to get the cartesian coordinates of the termini, from which you can easily calculate the projection onto some other vector, autocorrelation, or other projections.

Kind regards,
Erik

Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 23 Apr 2015, at 13:59, Smith, Micholas D. <smithmd at ornl.gov<mailto:smithmd at ornl.gov>> wrote:

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

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From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se>> on behalf of pratibha kapoor <kapoorpratibha7 at gmail.com<mailto:kapoorpratibha7 at gmail.com>>
Sent: Thursday, April 23, 2015 7:06 AM
To: gmx-users at gromacs.org<mailto: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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