THE EFFECTS OF TRUNCATING LONG RANGE FORCES ON PROTEIN DYNAMICS

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We have carried out a basic research project that considers the effects of truncating long range forces on protein dynamics. Based on seventy calculations of carboxymyoglobin we have shown that the method and distance of long range cutoff have a dramatic effect on overall protein behavior. The simulations in which long range forces are truncated by a shifted potential shows large rms deviations for cutoff criteria less than 14 Angstroms, and reasonable deviations and fluctuations at this cutoff distance or larger. Simulations using a switching function were investigated by varying the range over which electrostatic interactions are switched off. Results using a short switching function that switches off the potential over a short range of distances are poor for all cutoff distances. A switching function over a 5--9 Angstrom range gives reasonable results for a distant dependent dielectric, but not using a constant dielectric. Both the atom-atom and group-group truncation methods based on distance shows large rms deviation and fluctuation for short cutoff distances, while for cutoff distances of 11 Angstroms or greater, reasonable results are achieved. Although comparison of these to distance based truncation methods show surprisingly large rms deviations for the group-group truncation, contrary to studies of aqueous ionic solutions. The results of atom-atom or group -group list based simulations generally appear to be less stable than the distance based simulations, and require more frequent velocity scaling or stronger coupling to a heatbath. We hope that the results of these simulations provide assistance in choosing a method of truncating long range potentials in protein dynamics.