Galaxy |

GROMACS Radius of Gyration (version 2022+galaxy0)

Trajectory file:

In XTC or TRR format

Structure file:

In TPR format

Index (NDX) file:

Index file containing the molecules of interest

Index of group:

Index of group for calculating the radius of gyration - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).

Output format:

Format for output; either standard GROMACS XVG, or Galaxy tabular file.

Generate detailed log:

Generate detailed log information that can be summarized with ParseLog.

What it does

This tool computes the radius of gyration of a molecular structure, which provides an idea of how compact versus how open or extended the molecule's most commonly adopted conformation is, and how it changes throughout a trajectory. It can often be determined experimentally, so computing this from a simulation and comparing the results can also allow the researcher to verify the accuracy of the chosen force field for that particular system.

Input

TPR file of the simulated system.

XTC or TRR trajectory file from a prior simulation.

Index file generated using the 'Create GROMACS index files' tool (make_ndx).

Output

XVG file containing the radius of gyration at every frame of the trajectory.