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Introduction

Although MD simulation techniques are widely used in physics, chemistry and biology, their possibilities are often not fully exploited because of the lack of easy-to-use analysis tools. This is especially true for very complex systems which force most computational scientists to use standard program packages containing only very limited functionality to analyze MD trajectories.

In this NOTE we present the new release 3.0 of the modular program package nMOLDYN, which replaces the original version nMOLDYN 2.0, for the analysis of MD trajectories.

The program nMOLDYN was developed mainly for use in connection with neutron scattering experiment, although many of the quantities are also used in other contexts. The combination of neutron scattering experiments and MD simulations is a powerful tool to study the structure and dynamics of complex molecular systems. Neutron scattering is sensitive to time and space correlations of atomic positions on the ns time scale and the Å length scale [7,8]. These are exactly the time and space domains covered by classical MD simulations. On the length scale under consideration the neutron-target interaction can be modelled by pseudopotentials with zero range which are centered on the atomic nuclei of the targets. The coupling between neutron and target is described by so-called scattering lengths describing the strength of the neutron-nucleus interaction [7]. The differential scattering cross section can be expressed in terms of quantum time correlation functions of the spatially Fourier transformed particle density. The corresponding classical time correlation function can be easily obtained from MD simulations. This enables a direct comparison between simulated and measured neutron scattering intensities for classical systems if recoil effects in the scattering process are not dominant [9]. The experimental data can be used to test the quality of the MD force field which is the central input for the simulations [10,11,12,13]. Conversely, the simulated intensities allow a detailed analysis of the dynamical and structural behaviour of the system under consideration [14,15]. The latter is particularly important for complex systems for which an interpretation of the measured intensities in terms of simple analytical models is difficult, if not impossible.

The program package nMOLDYN allows neutron scattering intensities to be efficiently calculated from MD simulations. The calculation of various space and time correlation functions permits a detailed analysis of the structure and dynamics of the system under consideration. nMOLDYN contains modules for the calculation of dynamics-related, scattering-related and structure-related properties. In addition rigid body trajectories of subunits of the system can be extracted from molecular dynamics trajectory files. These subunits can be arbitrarily defined, their size can range from a few atoms to a whole domain in a macromolecule. From the rigid body trajectories angular correlation functions and reorientational correlation functions can be obtained.

The third generation nMOLDYN presented here, offers an interactive graphical user interface for standard calculations, highly flexible script-based processing for non-standard applications and a machine-independent compact binary file format. These improvements were made possible by the use of

1. python, a high-level object oriented langage [16,17];
2. NumPy, a python package needed for scientific computing [18];
3. NetCDF, portable binary file format and its corresponding library [5,6];
4. Scientific Python, an additional scientific computing library [20,21];
5. MMTK, a molecular simulation library [3,4].

All of these packages are developped and distributed following the Open Source principles [22]; anyone can use and improve them without being hindered by licensing restricitons. All the time-consuming algorithms use efficient implementations in C or in Pyrex, a language that allows to write code that mixes Python and C data types, and compiles it into a C extension for Python [23].

This NOTE is organized as follows:

Section 1 gives an overview of nMOLDYN.
Section 2 gives the instruction to install nMOLDYN properly in an existing python distribution.
Section 3 describes the different nMOLDYN file formats.
Section 4 describes how to set up and run an analysis in nMOLDYN from the Graphical User Interface (GUI).
Section 5 describes how to set up and run an analysis in nMOLDYN from the command-line interface.

Subsections

- New features in version 3.0
- User feedback

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