Gromacs (saving last frame as PDB or Gro)

  • Hello,
    I am running my simulation and selecting the trajectory option to save the result. Is there any way to save the last frame of the trajectory as a gro or pdb file out of the whole trajectory?
    This will solve both issues to solve the result as trajectory as well as the last final frame to be used for further analysis.
    Kindly also tell where all the results got saved during the whole SAMSON operation (because SAMSON does not ask for choice of directory for saving results)?

    Thank You

  • Dear @sudhir ,

    To save only the last frame in the trajectory into a PDB file, you can select a path corresponding to this trajectory and set the step to the last one in the Inspector (click Ctrl/Cmd + I to open the Inspector in SAMSON), this will update the structural model - it will correspond to the step you chose. Now you can select the structural model in the Document view and save only the selection as a PDB file, for that in the menu go to Selection > Save selection as and select the PDB format in the types of files.

    As for now, there is no direct way to save a .gro file from within SAMSON.

    The GROMACS Wizard Element saves the temporary files, including some gro files in a specific scratch folder in your user's directory, the path is different for different OS (Windows, Linux, Mac OS). You can either try looking for the Scratch/GROMACS on your system or check out the path to SAMSON's scratch folder by launching SAMSON-Core-Console executable version and checking for a line with SBGPath::getScratchPath() in the beginning of the console output. On Windows it will be something like: C:\Users\user\AppData\Local\OneAngstrom\SAMSON\DATA\0.8.3\Scratch.

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