[gmx-users] short-range eletrostatic energy of every aminoacid

Diogo Martins de Sá sadiogo at mol.bio.br
Mon May 25 20:38:07 CEST 2015

Hello guys,

I'd like to do make an energy matrix of every aminoacid of a simulation
of two interacting proteins. I know enemat can assess the matrix, but
for this I have to define energygroups in .mdp files. What would be the
easiest way to achieve this? 

I guess if I am going to find an easier way, I have to understand how
gromacs "finds" the energygroups I have written down in the .mdp file.
Lets say I manage to write down all the aminoacids I want in the
energygroups of the .mdp file. How would gromacs know where to look for
the atoms comprising each aminoacid? An index file, a topology file?

Thanks in advance.


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