7. Analysis¶
A typical analysis tasks reads the trajectory (XTC) or energy (EDR) file, computes quantities, and produces datafiles that can be plotted or processed further, e.g. using Python scripts. A strength of Gromacs is that it comes with a wide range of tools that each do one particular analysis task well (see the Gromacs manual and the Gromacs documentation).
7.1. Basic analysis¶
As examples, we perform a number of common analysis tasks.
7.2. More Gromacs tools¶
A number of interesting quantities and observables [1] can be calculated with Gromacs tools. A selection is shown below but you are encouraged to read the Gromacs manual and the Gromacs documentation to find out what else is available.
Selection of Gromacs analysis tools
The full list of Gromacs commands contains 98 different tools. A small selection of commonly used ones are shown here:
- gmx energy
- basic thermodynamic properties of the system
- gmx rms
- calculate the root mean square deviation from a reference structure
- gmx rmsf
- calculate the per-residue root mean square fluctuations
- gmx gyrate
- calculate the radius of gyration
- gmx mindist and gmx distance
- calculate the distance between atoms or groups of atoms (make a index file with gmx make_ndx to define the groups of interest). gmx mindist is especially useful to find water molecules close to a region of interest.
- gmx do_dssp
- Use the DSSP algorithm [Kabsch1983] to analyze the secondary structure (helices, sheets, …).
Footnotes
[1] | “Observable” is used in the widest sense in that we know an estimator function of all or a subset of the system’s phase space coordinates that is averaged to provide a quantity of interest. In many cases it requires considerable more work to connect such an “observable” to a true experimental observable that is measured in an experiment. |