I have a box let's say full of toluene, I want to measure the angle between toluene molecules versus distance. I think I should use "gmx gangle"; however I am a bit confused about how to select my groups. I am wondering if anybody has had a similar experience.
Any help is highly appreciated
Dear Ali Ghamartale
For using gangle you should create two vectors in the index file for two groups by make_ndx command.
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-gangle.html
Hope it helps
Yes, you have to use make_ndx to create index groups specifying the start and end points (probably atoms) of each vector you want to pass to gangle. And make sure you use the -n flag to include your index file or it will use the default groups instead of the ones you defined. Enter the group number of each index group you want, depending on what options you need, and hit ctr-D.
Aaron Feinstein Thank you so much for replying my question. I would like to ask my question more specific. I have 50 molecules in the box that can aggregate and I would like to see how they will approach and bond to each other. So I want the average angle between ever and each of them versus distance. I would appreciate you if you can reply to me more specific to my case.
Should I specify three atoms of each molecule in both group1 and group2?
If you use the option -seltype, you can define what kind of selection you want to use. For example, if you were doing a simulation with toluene you might want to measure an angle defined by two vectors between the rings of 3 molecules. You could use the "whole_mol_com" switch to say "define the heads and tails of these vectors as the centers of mass of each toluene atom" or whole_mol_cog to use the centroids. Then define your groups as whole toluene molecules.
If you're looking to average over a big group of different angles, I think you should use gmx angle, not gmx gangle.
As for finding the angles between every toluene in the system AND how they relate to intermolecular distance over time, that's harder to say. I think in that case you're heading into territory where you're better off trying to write something with, e.g., the python module mdtraj to analyze your trajectory using separate data files for angles and distances. Someone feel free to correct me if they can think of a single GROMACS program that can do this.
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