Galaxy | Tool Preview

Modify/convert and concatate GROMACS trajectories (version 2022+galaxy2)

Modify a trajectory or concatenate multiple trajectories?:

Input trajectory:

In XTC or TRR format; structure files with PDB or GRO format can also be used.

Input structure:

In PDB, GRO or TPR format.

Index (NDX) file:

In NDX format. Optional.

Index of group to save in the output:

Index of group to save in the output - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).

Index of group for centering:

Index of group for centering - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0). Leave blank if centering is not required.

Write each trajectory frame to a separate GRO or PDB file?:

Results will be stored as a Galaxy collection. Only has effect with PDB or GRO output, otherwise ignored

PBC treatment:

Unit cell representation:

Only has effect in combination with PBC treatment of mol, res or atom

Number of frames to skip:

This allows you to compress a trajectory file, by reducing the amount of frames written out into the new trajectory file.

Center for PBC and centering treatment:

Fit molecule to reference structure in the reference file?:

Output format:

Times

Time 0

Generate detailed log:

Generate detailed log information that can be summarized with ParseLog.

What it does

This tool allows manipulation of GROMACS trajectories, drawing on the trjcat and trjconv commands.

Input

One or more trajectory files (XTC or TRR)

Structure file (optional)

Various options can be set

Output

GROMACS trajectory or structure file (XTC, TRR, PDB, GRO)