A new algorithm to compute both the short-range (Lennard-Jones) and Coulomb forces in molecular dynamics based on the tree of clusters has been developed and incorporated into IMPACT. As far as we know, this work is new since until now the hierarchical algorithms have been used only to handle the long-range (electrostatic or gravitational) interactions. Although it is hard to estimate the asymptotic growth of this algorithm (it depends on both the number of particles N and the cutoff radius rc) preliminary results indicate that it scales like O(N) for fixed cutoff radius, contrary to the direct method which scales as O(N2). In previous work, we have implemented a parallel version of this method on the CM-5. We are now in the process of porting the code to the IBM

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Halgren, Thomas A; Murphy, Robert B; Friesner, Richard A et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750-9
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Baik, Mu-Hyun; Friesner, Richard A; Lippard, Stephen J (2003) Theoretical study of cisplatin binding to purine bases: why does cisplatin prefer guanine over adenine? J Am Chem Soc 125:14082-92
Baik, Mu-Hyun; Friesner, Richard A; Lippard, Stephen J (2002) Theoretical study on the stability of N-glycosyl bonds: why does N7-platination not promote depurination? J Am Chem Soc 124:4495-503
An, Yuling; Friesner, Richard A (2002) A novel fold recognition method using composite predicted secondary structures. Proteins 48:352-66
Gallicchio, Emilio; Zhang, Linda Yu; Levy, Ronald M (2002) The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. J Comput Chem 23:517-29
Friesner, R A; Dunietz, B D (2001) Large-scale ab initio quantum chemical calculations on biological systems. Acc Chem Res 34:351-8
Gherman, B F; Dunietz, B D; Whittington, D A et al. (2001) Activation of the C-H bond of methane by intermediate Q of methane monooxygenase: a theoretical study. J Am Chem Soc 123:3836-7
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