[gmx-users] g_angle between center of mass of three groups

jagannath mondal jmondal2004 at yahoo.co.in
Wed Nov 4 16:41:49 CET 2009

Thanks, But I guess the g_angle -ov option will give me an average angle for many different groups. 
That will not be same as the angle between center of masses of different group .
For example If I have a molecule CH3-CH2-CH3, g_angle -ov can give me an average over angle  H-C-H and C-C-C .  But what I want is the angle CH3-CH2-CH3 .

So, I was wondering whether you can clarify a bit on how I can get it.

--- On Wed, 4/11/09, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] g_angle  between center of mass of three groups
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Wednesday, 4 November, 2009, 9:00 AM

jagannath mondal wrote:
> Hi,
>   I know that g_dist gives the distance between the center of masses of  two groups.  But, I wanted to know whether it is possible to calculate angle between center of masses of three groups or not . I am not sure whether g_angle can calculate the angle between center of masses of three groups.    If not, In that case,  can anyone suggest suggest any other alternative ?

You should start by reading g_angle -h and g_sgangle -h. g_angle will calculate the average over a group of angles, which is similar to what you want.

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