We present the GalMer database, a library of galaxy merger simulations, that has been produced and made available to users by means of tools compatible with the Virtual Observatory (VO) standards adapted specially for this theoretical database. To investigate the physics of galaxy formation through hierarchical merging, it is necessary to simulate galaxy interactions varying a large number of parameters, e.g. morphological types, mass ratios, orbital configurations. On the one hand, these simulations have to be performed in a cosmological context, capable of providing a large number of galaxy pairs, with boundary conditions given by the large-scale simulation. On the other hand, the resolution has to be high enough on galaxy scales, to provide realistic physics. The GalMer database is a library of thousands of simulations of galaxy mergers at moderate spatial resolution and represents a compromise between considering a diverse range of initial conditions and optimising the details of underlying physics. We provide all coordinates and data of simulated particles in FITS binary tables. The main advantages of the database are VO access interfaces and value-added services that allow users to compare the results of the simulations directly to observations: stellar population modelling, dust extinction, spectra, images, visualisation using dedicated VO tools. The GalMer value-added services can be used as a virtual telescope producing broadband images, 1D spectra, 3D spectral datacubes, thus enhancing the utility of our database to observers. We present several examples of the GalMer database scientific usage obtained by analyzing simulations and modelling their stellar population properties, including: (1) studies of the star formation efficiency in interactions; (2) creation of old counter-rotating components; (3) reshaping metallicity profiles in elliptical galaxies; (4) orbital to internal angular momentum transfer; (5) reproducing observed colour bimodality of galaxies.