Visualization Software

Some programs that are useful for visualizing either a trajectory file and/or a coordinate file are:

  • VMD - a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Reads GROMACS trajectories.
  • PyMOL - capable molecular viewer with support for animations, high-quality rendering, crystallography, and other common molecular graphics activities. Does not read GROMACS trajectories in default configuration, requiring conversion to PDB or similar format. When compiled with VMD plugins, trr & xtc files can be loaded.
  • Rasmol - the derivative software Protein Explorer (below) might be a better alternative, but the Chime component requires windows. Rasmol works fine on Unix.
  • Protein Explorer - a RasMol-derivative, is the easiest-to-use and most powerful software for looking at macromolecular structure and its relation to function. It runs on Windows or Macintosh/PPC computers.
  • Chimera - A full featured, Python-based visualization program with all sorts of features for use on any platform. The current version reads GROMACS trajectories.
  • Molscript - This is a script-driven program form high-quality display of molecular 3D structures in both schematic and detailed representations. You can get an academic license for free from Avatar.

Also if appropriate libraries were found at configure-time, gmx view can useful.

Topology bonds vs Rendered bonds

Remember that each of these visualization tools is only looking at the coordinate file you gave it (except when you give gmx view a tpr file). Thus it’s not using your topology which is described in either your top file or your tpr file. Each of these programs makes their own guesses about where the chemical bonds are for rendering purposes, so do not be surprised if the heuristics do not always match your topology.

Extracting Trajectory Information

There are several techniques available for finding information in GROMACS trajectory (trr, xtc, tng) files.

  • use the GROMACS trajectory analysis utilities
  • use gmx traj to write a xvg file and read that in an external program as above
  • write your own C code using gromacs/share/template/template.cpp as a template
  • use gmx dump and redirect the shell output to a file and read that in an external program like MATLAB, or Mathematica or other spreadsheet software.

External tools to perform trajectory analysis

In recent years several external tools have matured sufficiently to analyse diverse sets of trajectory data from several simulation packages. Below is a short list of tools (in an alphabetical order) that are known to be able to analyse GROMACS trajectory data.

Plotting Data

The various GROMACS analysis utilities can generate xvg files. These are text files that have been specifically formatted for direct use in Grace. You can, however, in all GROMACS analysis programs turn off the Grace specific codes by running the programs with the -xvg none option. This circumvents problems with tools like gnuplot and Excel (see below).

Note that Grace uses some embedded backslash codes to indicate superscripts, normal script, etc. in units. So “Area (nmS2N)” is nm squared.

Software

Some software packages that can be used to graph data in a xvg file:

  • Grace - WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace runs on practically any version of Unix-like OS, provided that you can satisfy its library dependencies (Lesstif is a valid free alternative to Motif). It is also available for the other common operation systems.

  • gnuplot - portable command-line driven interactive data and function plotting utility for UNIX, IBM OS/2, MS Windows, DOS, Macintosh, VMS, Atari and many other platforms. Remember to use:

    set datafile commentschars "#@&"

    to avoid gnuplot trying to interpret Grace-specific commands in the xvg file or use the -xvg none option when running the analysis program. For simple usage,:

    plot "file.xvg" using 1:2 with lines

    is a hack that will achieve the right result.

  • MS Excel - change the file extension to .csv and open the file (when prompted, choose to ignore the first 20 or so rows and select fixed-width columns, if you are using German MS Excel version, you have to change decimal delimiter from “,” to “.”, or use your favourite *nix tool.

  • Sigma Plot A commercial tool for windows with some useful analysis tools in it.

  • R - freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.

  • SPSS A commercial tool (Statistical Product and Service Solutions), which can also plot and analyse data.

Micelle Clustering

This is necessary for the gmx spatial tool if you have a fully-formed single aggregate and want to generate the spatial distribution function for that aggregate or for solvent around that aggregate.

Clustering to ensure that the micelle is not split across a periodic boundary condition border is an essential step prior to calculating properties such as the radius of gyration and the radial distribution function. Without this step your results will be incorrect (a sign of this error is unexplained huge fluctuations in the calculated value when the visualized trajectory looks fine).

Three steps are required:

  • use trjconv -pbc cluster to obtain a single frame that has all of the lipids in the unit cell. This must be the first frame of your trajectory. A similar frame from some previous timepoint will not work.
  • use grompp to make a new tpr file based on the frame that was output from the step above.
  • use trjconv -pbc nojump to produce the desired trajectory using the newly produced tpr file.

More explicitly, the same steps are:

gmx trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
gmx grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
gmx trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump