MULTIHYDRO and MONTEHYDRO: Conformational search and Monte Carlo calculation of solution properties of rigid or flexible bead models

Abstract

A computer program, MULTIHYDRO, has been constructed for the calculation of hydrodynamic coefficients and other solution properties of multiple possible conformations of a bead model. With minimal additional programming to describe the model under study, this program interfaces efficiently with HYDRO [J. García de la Torre, S. Navarro, M. López Martínez, F. Díaz, J. Cascales, HYDRO: a computer software for the prediction of hydrodynamic properties of macromolecules, Biophys. J. 67 (1994) 530–531] [3] for the calculation of solution properties, including hydrodynamic coefficients, radius of gyration, covolume, etc. A useful application is the conformation search of rigid macromolecules, because many possible conformations can be evaluated in a single run of the program. In this paper we also pay attention to the properties of flexible macromolecules, in the so-called Monte Carlo rigid-body approximation, which is virtually exact for the simpler solution properties. The theoretical aspects of the procedure are described, and we show how MULTIHYDRO can be employed for this calculation. However, for flexible molecules, a more general simulation scheme is importance-sampling Monte Carlo generation. We describe how this procedure is implemented in another computer program, MONTEHYDRO. Examples of the usage of these tools are provided.