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?
Mark
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