computer modeling in molecular biology.pdf

4 Molecular Dynamics and Free Energy Calculations 67Figure 4-2. The TIP3P water molecule [40]. b is the value of the (fixed) 0 - H bond lengthin angstrom, 0 is the H-0-H (fixed) bond angle value in degrees. qaH are the partialcharges assigned to the nuclei (in fraction of elementary charge unit [el = 1.6 lo-'' C). Asingle Lennard-Jones interaction center is positioned at the oxygen nucleus, E is the well depthin kcal/mol and o the interatomic distance at which the potential is zero (in angstrom).4.2.1.3 Treatment of Long-Range Coulombic InteractionsCoulombic interactions vary as rij -' and therefore belong to the catagory of longrange interactions [44]. One of the major problems in simulating dilute protein solutionswhich contain a large polar water phase, is to achieve an adequate treatmentof such interactions. To save computer time a common practice is to neglect interactionsbetween atoms that are further apart than a given cutoff distance, rc, whichis usually no more than 7-10 A. Whereas van der Waals interactions are negligibleat such distances, Coulomb interactions still make substantial contributions, andsimply applying the cutoff rule causes spurious fields that influence the behavior ofthe system in a non-physical way. To avoid this problem a radial atom-atom cutoffdistance of 7 A was used here together with a truncation scheme which modifies theCoulomb interactions over the entire distance range so that it smoothly decays tozero at the cutoff distance:U'(r)= U(r).S(r) (4-9)