To get the bonded energy terms of one molecule in your system you
have to generate a trajectory file containing this molecule only:
trjconv -f full.trr -n molecule.ndx -o molecule.trr
and then rerun the simulation using a tpr containing only the topology
of your molecule:
grompp -f molecule.md
Hi, all,
I did a simulation on a system which had more than one molecule in it. After
the simulation, I want to check the bond/angle/dihedral energy of one molecule
in the system.
So I set a energy_grp named DNA in the mdp file, and used the command g_energy
to calculate the energy on the ener
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