05 July 2019 3 3K Report

I created .prmtop topology and .inpcrd coordinate files in tleap, and then I ran minimization, heating, and equilibration steps, and then 10 ns of production with pmemd in AMBER 14 and created .rst and .mdcrd files for my protein-ligand complexes, I noticed when trying to view the trajectory in VMD, it looked like my complex went out of the box during some steps, and I just want to make sure I'm looking at the files correctly since I'm new to MD simulations. In VMD, I used the command "vmd complex.pdb", and then loaded the complex.prmtop file and then the complex.inpcrd file, and then the min.rst, heat.rst, and equil.rst files, and then the production.rst files for each of the 10 nanoseconds. Is this the correct way to view trajectories in VMD? What is the purpose of visualizing the trajectory for MD simulations?

When trying to load the files for one of my complexes in VMD, I noticed that my complex.inpcrd, min.rst, and equil.rst files jumped around on the screen into different positions, but after the prod.rst files, it stayed relatively in place. I also noticed that for some of my complexes, the RMSD didn't converge completely after 10 ns because there were very sharp sudden peaks in my RMSD graphs that I created with cpptraj, so I was wondering if the issue could just be my settings during the MD simulations, or if I'm selecting the wrong files to load into VMD. Should I load the .mdcrd files instead of .rst, or would there not be a difference?

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