i have run a simulation for a protein (minimization, equilibration and production). in minimization step, the potential energy value in the log file is minimized at temperature = 0 K. in the equilibration step, the system is heated (temperature = a target value) so the potential energy is increased (become less negative) and the kinetic energy in increased from zero.
so what does the potential energy represent? is it related to the number of bonds in the protein only or the protein + water + ions?
Thanks
It depends on the force field you used in your program, so if you used CHARMM 36 FF you have to check what is the potential energy equation in the FF.
Usually, the potential energy is an additive function of bond length, angles, dihedrals, Colomb, and van der Waals. This function is calculated for the system (protein + water + any additives).
Abdo A Elfiky so what is the effect of the minimization step on potential energy? when I checked the log file I noticed that the potential energy decreases and this did not affect the structure very much. why did it become more negative?
The minimization in the potential energy is the result of changing the bond length, angle, dihedral , etc... You can superimpose the structure before and after the minimization to see the difference. If you started with a well-optimized structure the changes will be small.
Keep in mind that the CHARMM GUI first minimize the water then the whole system (water, protein, and ions).
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