[gmx-users] Generalized Energy Groups

tca1 tca1 at rice.edu
Wed Apr 17 01:13:29 CEST 2019

Hi all,

I'm currently trying to analyze the energy balance of a trajectory  
where I see various kinds of spatial partitioning of my molecules. I'd  
like to be able see a breakdown based on spatial group and atom type.  
However, I only know which molecules end up in which spatial region  
after the trajectory is complete (so I can't just declare the groups  
beforehand in my mdp file).

Likewise, I want some sort of intersection of atom type and spatial  
group for my analysis, but it seems that this sort of selection is  
more general than what I could do with the energy groups in an mdp  
file, and I can't use a more general index file with the gmx energy  
command post-simulation.

Is there any way to do something like mdrun -rerun with more general  
groups of atom indices to get a customized breakdown of energetic  
interactions from a trajectory, or is this type of thing just not  

Tom Allen

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