Gromacs system modification

This protocol performs modifications over a Gromacs System, specially over its trajectory.

The modifications include:

  • Cleaning: removing waters and ions

  • Fitting: Fit trajectory to initial structure

  • Dropping: Cut a trajectory, saving only from first to last specified times

  • Subsampling: Subsample trajectory frames

  • Filtering: Perform low/high pass filters on trajectory frames

Input

Note

All parameters include a help button that gives further information for each of them.

Gromacs system modification form 1

The result of this protocol is a GromacsSystem, containing the modified Gromacs files and trajectory. The user can visualize the complex using Analyze Results.

Test

This protocol has an integrated test that can be run using the following command:

scipion3 tests gromacs.tests.tests.TestGromacsTrajMod