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 also 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).

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

Contacts.AA.pl (10/26/08) determines the number of native contacts formed as a function of time for your trajectory for an All-atom SBM (i.e. 6-12 interactions for contacts). **CAUTION** This script allows you to define contacts as any native pairs within CUTOFF times the native distance. Currently, CUTOFF=1.5. This may not be the definition you want to use. Always double check the value of CUTOFF before using this script. Also, please read the comments inside of the script to make sure you use it properly.

Contacts.CA.pl (11/02/09) determines the number of native contacts formed as a function of time for your trajectory for an C-alpha SBM (i.e. 10-12 interactions for contacts). **CAUTION** This script allows you to define contacts as any native pairs within CUTOFF times the native distance. Currently, CUTOFF=1.2. This may not be the definition you want to use. Always double check the value of CUTOFF before using this script. Also, please read the comments inside of the script to make sure you use it properly.

WHAM.jar (9/21/2016) 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 manual (PDF).

Contributed Tools

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.


Please direct questions and comments to info@smog-server.org.
Page created and maintained by Jeff Noel and Paul Whitford