[gmx-users] how to create a index file for angle calculation

[Dallas Warren]

It sounds like you are measuring the angle between two planes.  You then
need to tell gangle that you are measuring planes (B in
http://manual.gromacs.org/documentation/current/_images/sgangle.png) using
-g1 plane -g2 plane, rather than the angle between three points (
http://manual.gromacs.org/documentation/current/_images/angle.png) using
-g1 angle -g2 none.  You are doing the latter by default.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Mon, 14 Jan 2019 at 23:19, SHAHEE ISLAM <islamshahee at gmail.com> wrote:

> hi,
> if i want to calculate angle between two group,then the group will be
> in same file or in different file.because when i am using this command
> gmx gangle -f md-0-1-300k-pbc.xtc -n index.ndx -dt 2000 -oall angle.xvg
>  putting the two group (1 and 2 both) in same idex file , i am getting
> the values for group1 and group2 separately.but i want to calculate
> the angle between the two groups. both two groups contains three
> residue.
> thanking you
> shahee
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