Trpcage contains 20 amino acid residues and is currently the smallest protein to display two state folding properties at room temperature. The small size of the protein makes it an ideal candidate for computational folding simulations. All fully unrestrained molecular dynamics simulations were carried out with AMBER version 8.0 to calculate the total energy, RMSD, end-to-end distance and structure using VMD program. Initially fully unfolded Trpcage in solution formed a stable folded structure after 100 ns simulations, and RMSD analysis indicated that the final simulation structures were quite comparable to the NMR structures. Simulation result of three mutants of Trpcage in solution showed that enhancing the hydrophobic properties in the cage regions (core or inside of the protein molecule) increased the stability of protein molecule as evidenced by a much lower free energy and a smaller RMSD compared with NMR structure of native protein, while an increase in the hydrophobicity in the terminal region led to an unstable state for the protein molecule. This is in agreement with the experimental studies that support the hypothesis that protein is likely to be stabilized by forming a hydrophobic core inside to avoid contacting H2O molecules. Simulation results of protein that is initially either in a linear structure (fully denatured state, type I), or in a compact structure (native state, type II), on silica surface at short times reveal that both types of molecules quickly move close to the surface, followed by a conformational change. Type I protein molecule quickly formed some á helical structure after its interaction with the surface, while type II protein molecule experienced a much slower loss of its tertiary structure, while still maintaining a certain secondary structure. The results indicated that no matter what the initial structure is, protein molecule reached the same equilibrium state. The effects of temperature, pH and ionic strength on the conformation of Trpcage adsorbed on silica surface are reported.