[gmx-developers] 6-12 and coulomb / energy / atom pairs
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.
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 -
Find what you are looking for with the Lycos Yellow Pages
More information about the gromacs.org_gmx-developers