Force Field Energy Evaluation (energy)

Evaluates classical molecular mechanics force field energy components in electron-volts ($\text{eV}$).

Mathematical Formulation

The total empirical potential energy is evaluated as:

$$U_{\text{total}} = E_{\text{bond}} + E_{\text{angle}} + E_{\text{vdw}} + E_{\text{coulomb}}$$

Where:

• $E_{\text{bond}} = \sum \frac{1}{2} k_b (r - r_0)^2$
• $E_{\text{angle}} = \sum \frac{1}{2} k_\theta (\theta - \theta_0)^2$
• $E_{\text{vdw}} = \sum 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right]$
• $E_{\text{coulomb}} = \sum \frac{1}{4\pi\varepsilon_0} \frac{q_i q_j}{r_{ij}}$

Usage

atoma energy <TARGET>

Example Output

============================================================
 Atoma Molecular Mechanics Energy Evaluation
============================================================
 Molecule:               Water (H2O) (H2O)
 Atoms / Bonds:          3 / 2
------------------------------------------------------------
 Bond Stretching (E_b):        0.004608 eV
 Angle Bending   (E_a):        0.000000 eV
 Van der Waals   (E_lj):       0.000000 eV
 Electrostatic   (E_el):       0.000000 eV
------------------------------------------------------------
 Total Potential (U):          0.004608 eV
============================================================