A potential for molecular simulation of compounds with linear moieties.

Area of Science:

• Computational chemistry
• Molecular modeling

Background:

• Traditional harmonic angle bending potentials exhibit discontinuous forces near 180°, causing numerical instabilities in molecular simulations.
• Linear molecular groups (alkynes, nitriles) and molecules (CO2) require specialized handling in force fields.

Purpose of the Study:

• To develop and validate a novel harmonic potential for accurately simulating linear angle bending.
• To improve the numerical stability and accuracy of biomolecular simulations involving linear geometries.

Main Methods:

• Derived an analytical force constant for the new linear angle potential from traditional potentials.
• Tested the new potential on alkynes, nitriles, and carbon dioxide, including liquid simulations.
• Investigated the impact of long-range Lennard-Jones interactions and cutoff distances on simulation stability.

Main Results:

• The new potential maintained linear group angles closer to 180° (within 2°) compared to traditional methods.
• Simulations of liquid CO2 required explicit long-range Lennard-Jones interactions for stability.
• A Lennard-Jones cutoff of 1.1 nm provided results comparable to Particle Mesh Ewald for other liquids.

Conclusions:

• The proposed linear angle potential offers improved stability and accuracy for molecular simulations.
• The findings highlight the importance of long-range interactions in simulating systems like liquid CO2.
• The new potential is applicable to free energy perturbation calculations, broadening its utility.