Hi all,
Is it necessary that the value of potential energy after relaxation will always be negative? Is it a fixed rule? I am doing a simulation of bio-polymers (carbohydrates) using the PCFF force field. But I am getting positive value after relaxation.
If you have any idea, please help me to know.
Thank you.
Sincerely,
Sharmi
Hi all,
Is it necessary that the value of potential energy after relaxation will always be negative? Is it a fixed rule? I am doing a simulation of bio-polymers (carbohydrates) using the PCFF force field. But I am getting positive value after relaxation.
It is not a requirement, but it depends on the specific force field. For systems with LJ + Coulomb + Bonds/Angles/Dihedrals/Impropers the Coulomb and LJ terms are usually dominant and favor configurations where the potential energy is negative. If the total potential energy is positive you have to look at which component is positive. That can provide an indication of possible problems, either with the topology data or the assignment of partial charges.
What does the pressure look like? How is energy conservation? How does the temperature evolve if you run without a thermostat?
In summary, it need not be negative, but that does not happen a lot, so this is a warning and one needs to take a closer look.
For sufficiently small volume/large density and also sufficiently large thermodynamic temperature, most potential energy models will give positive energy. However, the absolute value is less important than the difference relative to some well defined reference state e.g. energy of isolated bio-polymers or energy of perfect crystal.
Aidan