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  2. Running Wales Group software on Windows 7 - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Running_Wales_Group_software_on_Windows_7
    New packages can be selected later by running the setup wizard again.
  3. Removing minima and transition states from the database - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Removing_minima_and_transition_states_from_the_database
    6 Jan 2021: First off back up the directory. The minima specified in files min.remove and ts.remove are removed and new files min.data.removed, ts.data.removed, min.A.removed,
  4. Biomolecules in the energy landscape framework - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Biomolecules_in_the_energy_landscape_framework
    The new libraries are found in the AMBERTOOLS/dat/leap/lib directory, you will need to copy them to your AMBER version (AMBER12 or newer!).
  5. Using BHINTERP to find minima between two end points - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Using_BHINTERP_to_find_minima_between_two_end_points
    6 Jan 2021: Often they are initial and final structures of studied path or reaction (however, here reaction means geometrical change in the system, not breaking and forming new bonds). ... overwrite! Update: new version of PATHSAMPLE does not overwrite this file,
  6. Creating movies (.mpg) of paths using OPTIM - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Creating_movies_(.mpg)_of_paths_using_OPTIM
    6 Jan 2021: If this doesn't help, then the NEWCONNECT commands in odata will tell OPTIM to try to bridge the gap by finding new TSs in the usual way to form a
  7. Using VMD to display and manipulate '.pdb' files - CUC3

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Using_VMD_to_display_and_manipulate_%27.pdb%27_files
    6 Jan 2021: Formyl. Vinyl. Chloride. Hydroxyl. Methyl. Those you can start a new molecule from are:.
  8. Loading OPTIM's min.data.info files into PATHSAMPLE - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Loading_OPTIM%27s_min.data.info_files_into_PATHSAMPLE
    min.data.info.initial. In a new directory copy the following files:. coords.inpcrd, coords.prmtop, min.data.info.initial, perm.allow, pathdata.
  9. Removing minima and transition states from the database - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Removing_minima_and_transition_states_from_the_database
    First off back up the directory. The minima specified in files min.remove and ts.remove are removed and new files min.data.removed, ts.data.removed, min.A.removed,
  10. GMIN - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/GMIN
    The program knows many different empirical potentials, and it is straightforward to add new systems. ... symmetry.f. mdiff is used to test whether a generated symmetry operation is new.
  11. Getting started with SLURM - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Getting_started_with_SLURM
    Change 'jwrm2' to your own username. We copy only the files GMIN needs in order to run, then change to the new directory. ... the files back and adds new stationary points to the database, then deletes the temporary directory.

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