I have a gromacs system of C60 fullerene particles dispersed in PMMA chains. The potential energy of the system turns out to be positive. Is this normal? (I did test both the components separately and the energy of the combined system is lower than the sum of the energy of the two components taken separately)
This outcome just means the magnitude of the bonded interactions (strictly positive) outweighs comparatively weak nonbonded interactions.
Thanks a lot for the quick reply, Dr. Lemkul. However, for my system, even the non-bonded energies are positive for both the combined system as well as the individual components taken separately. I am not sure if this is physical, as if all the energies are positive, then what is holding the system together?
Does your system expand over time? How has the system been parametrized and validated?
The system doesn't expand, energy minimization and equilibration goes smoothly with the density converging with time. I used a commercial package and a pretty common, general forcefield (Dreiding) to parametrize the system
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