# nMOLDYN 3

An overview of the current version of nMOLDYN.

nMOLDYN is an interactive analysis program for Molecular Dynamics simulations. It is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities. |

The current release 3.0 of nMOLDYN can compute the following quantities:

- coherent intermediate scattering function
- memory function for coherent scattering function
- dynamic structure factor
- incoherent intermediate scattering function
- elastic incoherent structure factor

*Quantities related to neutron scattering*

- mean-square displacement
- velocity autocorrelation function
- memory function for velocity autocorrelation function
- density of states
- angular velocity autocorrelation function (and its spectrum)
- reorientational correlation function

*Other quantities*

Moreover, nMOLDYN can construct modified trajectories from an input trajectory:

- rigid-body trajectories, in which the internal motions of the molecules (or parts thereof) are eliminated
- angular trajectories, which describe rigid-body motions by center-of-mass and orientational (quaternion) coordinates
- frequency-filtered trajectories, from which motions outside a specified frequency interval are eliminated

nMOLDYN has both a graphical user interface that is easy to use, and a command-line interface for experienced users. The latter is also appropriate for situations in which the graphical interface cannot be used for technical reasons (network restrictions etc.)

nMOLDYN uses the Molecular Modelling Toolkit (MMTK) and expects trajectories to be in MMTK format (netCDF files). Trajectory converters for CHARMM/X-PLOR/NAMD and DLPOLY trajectories are included in the distribution. A converter for AMBER trajectories is available separately.

All nMOLDYN calculations can be applied to a whole system or to arbitrary subsets. The most common subsets can be selected in the graphical interface from a list, less common selections can be specified by Python code via the command-line interface.