Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both fortran and C/C++ codes.

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The authors review the theory and the empirical evidence of damping of simple nuclear excitations. The excitations considered are the particle states and vibrational states. The particle damping phenomena include the fragmentation of single-particle levels, the systematics of neutron strength functions, and the optical absorption of elastic scattering. Information on the known collective vibrational states is summarized and compared with theory. A theoretical model that has found considerable success is based on a damping mechanism in which the simple excitations mix with the surface vibrations. This implies that the surface damping dominates for excitation energies below about 15 MeV. There is a close relation between the single-particle damping and the damping of collective vibrations. However, the vibrational damping is strongly suppressed by the coherence between the particle and the hole. While the model reproduces many of the observed features of the data rather well, it tends to underpredict the spreading width by as much as a factor of 2. Thus other degrees of freedom, not well understood at present, may play a role in the damping. CONTENTS I. Introduction II. Empirical Single-Particle Damping A. Spectroscopic study of single-particle fragmentation B. Single-particle states in the continuum 1. The neutron strength function 2. The optical model in elastic scattering III. Empirical Damping of Vibrations A. The giant dipole vibration B. Density vibrations: quadrupole, monopole, and octupole C. Spin vibrations IV. Theoretical Considerations A. The calculation of widths B. The nuclear response in RPA V. Theory of Single-Particle Damping A. Infinite nuclear matter Approximations

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