Next: Contents Contents

nMOLDYN User's Guide
Version 3.4

Eric Pellegrini, Paolo Calligari, Vania Calandrini
Konrad Hinsen, Gerald R. Kneller

October 6, 2009

Description

The nMOLDYN User's Guide describes how to use the various features of the MD analysis program nMOLDYN. This guide includes a description of the capabilities of the program, how to use these capabilities, the necessary input files and formats, and a comprehensive list of the analysis available in the program and how to set up an run these analysis.

1

### Abstract:

nMOLDYN is a modular program package for the analysis of Molecular Dynamics (MD) trajectories, especially designed for the computation and decomposition of neutron scattering spectra.

The current release 3.0 of nMOLDYN is an upgrade of the version nMOLDYN 2.0 [1], which extends the functionality of the original version nMOLDYN 1.0 [2]. It provides an improved user interface (both graphical/interactive and batch), and can be used as a tool set for implementing new analysis modules.

nMOLDYN allows one to calculate several dynamics quantities such as the mean-square displacement, the velocity autocorrelation function as well as its Fourier Transform (the density of states) and its memory functions, the angular velocity autocorrelation function and its Fourier transform, the reorientational correlation function ...Moreover it can compute several quantities related to neutron scattering such as the coherent and incoherent intermediate scattering functions with their Fourier transforms and their memory functions, the elastic incoherent structure factor, the static coherent structure factor or the radial distribution function. Additionally, the nMOLDYN package allows one to construct modified trajectories from an input trajectory; rigid-body trajectories, in which the internal motions of the molecules (or parts thereof) are eliminated, frequency-filtered trajectories, from which motions outside a specified frequency interval are eliminated, global motion filtered trajectory where the global rotation and translation are removed from the input trajectory ...

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, less common selections can be specified by Python code via the command-line interface.

As nMOLDYN 2.0, nMOLDYN 3.0 uses Molecular Modelling ToolKit (MMTK)[3,4], an Open Source program library for molecular simulation applications, and expects trajectories to be in MMTK format (Network Common Data Form (NetCDF) [5,6]). However, many trajectory converters are included in the distribution of nMOLDYN. nMOLDYN 3.0, was written by Eric Pellegrini.

- Contents
- List of Figures
- List of Tables
- List of Acronyms
- Introduction
  - New features in version 3.0
  - User feedback
- Installing nMOLDYN
  - Unix users
  - Windows users
- Input and output files
  - NetCDF file format
  - PDB file format
  - nMOLDYN preference file
  - nMOLDYN selection files
  - nMOLDYN autostart files
  - nMOLDYN input files
- Using nMOLDYNfrom the Graphical User Interface
  - The File menu
    - Load NetCDF file
    - Trajectory conversion
      - Amber to MMTK
      - CHARMM/X-PLOR to MMTK
      - DL_POLY to MMTK
      - Discover to MMTK
      - Forcite to MMTK
      - NAMD to MMTK