On the Use of United Atoms in Statistical Mechanical Simulations of Biomolecules

Abstract

Three different Molecular Dynamics simulations of calbindin D₉k, each lasting at least 160 ps, are compared in order to assess the effects of the “united atom” approximation in statistic mechanical simulations of macromolecules. One simulation is performed with the united atom concept applied to aliphatic CH _n -groups, while a second simulation treats all atoms explicitly using carbon and hydrogen parameters derived from crystal data of alkanes. In a third force field the hydrogen parameters have been changed so as to give an artificially strong attraction. The applicability of the force fields is judged from a comparison between simulated and experimental fluorescence depolarization and nmr relaxation data. The second force field is shown to be in best agreement with experiment and does also show the smallest rms deviation from the protein crystal conformation. The united atom force field is only slightly inferior and the artificial force field is moderately inferior as regards the comparison with experimental data.

Key Words:

• United atoms
• molecular dynamics
• calbindin