[gmx-developers] 6-12 and coulomb / energy / atom pairs

marcos lourenzoni lourenzoni at lycos.com
Tue Jul 20 20:34:48 CEST 2004

Dear Gromacs Developers,

I need evaluate the resulting (6-12 and coulomb) energy of the each atom of protein. The energy must be intra and intermolecular. 
The total number of protein atoms is: (natom)
The total number of protein atoms is: (nwater)
I need natom*nwater energy values of every simulation dt.
Another case.
I need natom*(natom-1) energies values.
I ‘ve seen the explanation of the g_enemat. 
The example in the mail: 1. [gmx-users] using g_enemat (score: 311)
I can´t understand the explanations of the groups in the index file and in the groups.dat. 
I know that I need to re-calculate the energies using –rerun, but I don´t understand the proceeding in the use of energy_groups option in these specific cases.
What is the “matrix of interaction energies”? Are there energy values to all atoms in the matrix? 
Can you pass a more detailed explanation about my doubts? 
Marcos R. Lourenzoni
Dept. of Chemistry
University of São Paulo – USP –
Ribeirão Preto – SP - 

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