[gmx-users] Potential energy of a single amino acid residu

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 10 12:17:55 CET 2009

Tom Venken wrote:
> Hello,
> I am trying to calculate the potential energy of an individual amino 
> acid and its interaction energy with the rest of the protein. I have 
> found another user with a similar problem: 
> http://www.gromacs.org/pipermail/gmx-users/2007-May/027114.html
> so I tried to follow the same procedure. An index-file was made 
> containing a group with the specific residu (r_8 in this case) and a 
> group of the rest of the protein without this residu (Protein_&_!r_8). 
> The mdp-file was changed as well, now containing:
> energygrps                                =    r_8
> energygrps_excl                           =    Protein_&_!r_8 non-Protein
> so basically only the energy of r_8 would be calculated with the 
> following commands:
> grompp -f ppmd_r8.mdp -c mdwater.pdb -p topol.top -o topol_md_r8.tpr -t 
> traj_mdwater.trr -n r8.ndx
> mdrun -s topol_md_r8.tpr -c md_r8.pdb -e ener_md_r8.edr -rerun 
> traj_md.trr (thus feeding the trajectory again but now with the new 
> selection)
> then g_energy -f ener_md_r8.edr -s topol_md_r8.tpr -o Epot_r8.xvg
> Unfortunately the output still gives me the energy of the whole protein 
> and not of the specific residu. Any idea of what went wrong?

So of what groups did g_energy suggest you could get output?


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