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

Berk Hess gmx3 at hotmail.com
Wed Nov 4 16:51:02 CET 2009


In principle g_traj -oxt -com would give you a trajectory with the COM's, you would then need a pdb or tpr
with the COM's as well. But in 4.0.5 there is a bug in g_traj when writing many COM's. This will be fixed in 4.0.6.

A, maybe simpler, solution, if your system runs fast, it to add COM virtual-sites to your atomistic topology,
which will then also appear in your trajectory.
Look in the manual on how to construct such virtual sites.


Date: Wed, 4 Nov 2009 21:11:49 +0530
From: jmondal2004 at yahoo.co.in
Subject: Re: [gmx-users] g_angle  between center of mass of three groups
To: gmx-users at gromacs.org

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>
 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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