United versus All Atom Force Fields

Because of the restricted availability of computational resources, some force fields use United Atom types. This type of force field represents implicitly all hydrogens associated with a methyl, methylene, or methine group. The van der Waals parameters for united atom carbons reflect the increased size because of the implicit (included) hydrogens. 

United Atom force fields are used often for biological polymers. In these molecules, a reduced number of explicit hydrogens can have a notable effect on the speed of the calculation. Both the BlO-t and OPUS force fields are United Atom force fields. AMBER contains both a United and an All Atom force field. 

Caution If you are new to computational chemistry, do not use United Atoms for AMBER calculations. This HyperChem option is available for researchers who want to alter atom types and parameters for this force field. 

Force field calculations often truncate the non bonded potential energy of a molecular system at some finite distance. Truncation (nonbonded cutoff) saves computing resources. Also, periodic boxes and boundary conditions require it. However, this approximation is too crude for some calculations. For example, a molecular dynamic simulation with an abruptly truncated potential produces anomalous and nonphysical behavior. One symptom is that the solute (for example, a protein) cools and the solvent (water) heats rapidly. The temperatures of system components then slowly converge until the system appears to be in equilibrium, but it is not. 

Arelatively simple method for alleviating some of the nonphysical behaviors caused by imposing a nonbonded cutoff is to use a potential switching function (equation 14). 

---

United atom force fields (see United versus All Atom Force Fields on page 28) are sometimes used for biomolecules to decrease the number of nonbonded interactions and the computation time. Another reason for using a simplified potential is to reduce the dimensionality of the potential energy surface. This, in turn, allows for more samples of the surface. 

---