WebbStep 1: Run short MD simulation of the protein system. Step 2: Checking results for the final step of the setup process, the free MD run. Plotting Root Mean Square deviation (RMSd) and Radius of Gyration (Rgyr) by time during the free MD run step. Building Blocks used: sander_mdrun from biobb_amber.sander.sander_mdrun. WebbAMBER comes with a simple program to generate standard canonical α- and β-duplex geometries of nucleic acids. The program nucgen will build cartesian coordinate …
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Molecular Dynamics Simulation
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