Gromacs - Spoken Tutorials - Assignments
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For assignment activity, please do the following.


1. Answer the following question.

2. Can 1AKI.pdb be aligned using npt.gro with the 'measure fit' command?

3. Explain the reasoning and demonstrate it.

4. Create a new representation for npt.gro molecule.

5. In Selected atoms enter, water and within 2 of protein.

6. This displays water molecules present only within 2 Angstrom of the protein.

7. Play the trajectory and notice the movement of water molecules.