nMOLDYN

If you're in the market for an interactive analysis program for Molecular Dynamics (MD) simulations, nMOLDYN should definitely be on your list. This software has been designed specifically for the computation and decomposition of neutron scattering spectra, but is also capable of computing other quantities.

One of the things that sets nMOLDYN apart is its ability to compute numerous quantities related to neutron scattering, including coherent intermediate scattering function, memory function for coherent scattering function, dynamic structure factor, incoherent intermediate scattering function, and elastic incoherent structure factor. Additionally, nMOLDYN can compute mean-square displacement, velocity autocorrelation function, memory function for velocity autocorrelation function, density of states, angular velocity autocorrelation function (and its spectrum), and reorientational correlation function.

But that's not all. nMOLDYN can also construct modified trajectories from an input trajectory, including rigid-body trajectories, angular trajectories, and frequency-filtered trajectories.

And the best part? nMOLDYN has both a graphical user interface and a command-line interface, making it easy for users of all levels of experience to work with. The software uses the Molecular Modelling Toolkit (MMTK) and includes trajectory converters for various formats, including CHARMM/X-PLOR/NAMD and DLPOLY.

For those who want to work with specific subsets, nMOLDYN offers the option to apply calculations to a whole system or arbitrary subsets, with the ability to specify less common selections using Python code via the command-line interface.

Finally, nMOLDYN is cross-platform and should work with all major variants of Unix and Windows. With minimal system-specific code, porting nMOLDYN to other systems should be simple. All in all, nMOLDYN is an excellent choice for those who need powerful and flexible MD simulations analysis software.