Multicanonical molecular dynamics (MD) is a powerful technique for sampling conformations in rugged potential surfaces, and has been applied to various systems. However, because of the practical difficulty in the iterative refinement of the multicanonical potential function, E-mc, a multicanonical MD has not yet been applied to a large system such as a globular protein in explicit solvent. We propose a method to evaluate E-mc for a protein in water without the iterative refinement process. The method was applied to the system of a protein, chymotrypsin inhibitor 2 (Ci2), in explicit water, composed of 11 330 atoms. We successfully produced a flat energy distribution covering the energy range corresponding to temperatures from 290 to 400 K. A 10-ns trajectory of the multicanonical MD simulation revealed that Ci2 adopts three different conformations in the long loop (residues 54-63), whereas a 10-ns trajectory of the conventional canonical MD simulation found only one conformation near the initial structure. These results indicate that a multicanonical MD with the method of evaluating E-mc is an efficient tool for enhancing the conformational sampling of the native structures of a protein in solution. (C) 2003 American Institute of Physics.