Step 3: Analyze your trajectory

Visualizing your trajectories: VMD is our favorite software for molecular dynamics visualization. It also provides a variety of easy to use GUI tools for trajectory analysis. To watch a Gromacs trajectory in VMD, simply load the .gro (coordinate) file and then select "load data into molecule" and load the .xtc or .trr (Gromacs trajectory files) into the .gro structure. If you prefer to load the structures from the command line, issue "vmd GRO_FILE.gro XTC_FILE.xtc". This will load the xtc file into the gro structure.

Calculating quantities from your simulations: Gromacs includes a large number of analysis programs with their distribution. Many produce text files formatted for use with Grace (a very powerful 2-D plotting tool). We have also been pleased with mdtraj, which has a large user base that makes many extensions available for free.

Additional scripts/programs: Scripts for tasks not easily available through Gromacs and VMD will be posted here over time. Contributed tools are always appreciated.

WHAM (version 1.10 Jan 2021) An implementation of weighted histogram analysis that is tailored for use with SMOG to compute thermodynamic quantities. Includes options to remove harmonic umbrella biases. Computes F(Q), F(Q1,Q2), Cv(T), Q(T), Q1(Q2) and many others. Functionality is described in the SMOG 2 Manual. Examples and source code can be found in the SMOG 2 distribution.

Contributed Tools

g_kuh - calculates Q, the fraction of native contacts for a trajectory (.xtc). Found in either of the SMOG enhanced Gromacs versions: 4.5.3 or the 5.0.4. Documentation can be found here.

PyWham (2/10/15) Another implementation of the Weighted Histogram Analysis Method written in Python. Features include, but are not limited to, free energy in multiple dimensions, umbrella bias removal and free energy perturbation, ensemble average of a user-defined quantity, customization of data input methods. Documentation and examples are included in the download package. Direct questions to li.sun@rice.edu.

This resource is provided by the Center for Theoretical Biological Physics.
Please direct questions and comments to info@smog-server.org.
Page created and maintained by Jeff Noel and Paul Whitford