In this paper, we describe the design and implementation of a message-passing algorithm which enables the Empirical Conformational Energy Program for Peptides (ECEPP/3) and related programs to run efficiently on the IBM RISC System/6000 POWERparallel System (SP2). Either the Message Passing Library (MPL) or the Message Passing Interface (MPI) can be used on the SP2; the MPI version also runs on the SGI Power Challenge computer. Some performance data are presented.

Implementation of ECEPP-Based Programs on the IBM SP2 and the SGI Power Challenge Computers

A recently proposed formulation developed for the study of molecular associations (E. Iglesias, T.L. Sordo and J.A. Sordo, Comput. Phys. Commun., 67 (1991) 268) was used to study a variety of systems: (H 2 O) n , (C 6 H 6 ) n , C 6 H 6 (H 2 O) n , CH 3 OH-(H 2 O) n , neutral glycine-(H 2 O) n , neutral serine-(H 2 O)n, glycine zwitterion-(H 2 O) n and serine zwitterion-(H[in2 O) n . The results show that the method, which makes use of pair potentials from ab initio calculations, provides energetic and structural information that is in satisfactory agreement with Monte Carlo simulations, at a much lower computational cost.

Molecular associations from ab initio pair potentials

A recently proposed formulation developed for the study of molecular associations was used to analyse the solutewater interaction (solvation) of the 20 commonly occurring amino acids. As a direct application of the computational results, a new scale of hydrophilicities is proposed and compared with other scales reported in the literature. Satisfactory agreement was found between the new scale and the experimental scale obtained by Wolfenden et al. (R. Wolfenden, L. Andersson, P.M. Cullis and C.C.B. Southgate, Biochemistry, 20 (1981) 849).

Molecular associations from ab initio pair potentials: Part 2. A new hydrophilicity scale for amino acids

Distribution of hydrogen-bonded rings in pure liquid water and methane solution by a Monte Carlo method

The effect of an external electric field on the structure of liquid water using molecular dynamics simulations

Monte Carlo treatment of hydration of models for side chains of proteins

Molecular inclusion by the new amide host molecule (TMB) has been reconsidered by calculating the crystal stabilization energies for the guest molecules in the TMB + guest system from the simple intermolecular potential functions of Caillet and Claverie. Water, ethylene glycol, methanol, and ethanol have been employed as guest molecules and their relative stabilities have been considered. Water has been found to be the most suitable guest molecule in the TMB + guest system. It also has been found that the guest host interaction is the most important contributor in determining the relative stabilities of the guest molecules in the TMB + guest system, but the guest guest interaction is very important, too. Moreover, the electrostatic interaction has been found to be the most important contributor to the total interaction energy in the TMB + guest system.

Theoretical study of the inclusion properties of 1,2,4,5-tetra(morpholinocarbonyl)benzene

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Monte Carlo treatment of hydration of models for side chains of proteins

Distribution of hydrogen-bonded rings in pure liquid water and methane solution by a Monte Carlo method

Theoretical study of the inclusion properties of 1,2,4,5-tetra(morpholinocarbonyl)benzene