A primer on molecular dynamics - by Abhishaike Mahajan
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7.8k words, 36 minutes reading time
Introduction How does MD work in practice? System Definition Force Fields The basic definition The details Energy minimization + equilibration Production simulation Interesting miscellaneous things Bypassing small timescales Quantum effects Free energy calculations Case studies Discovery of lirafugratinib (RLY-4008), a highly selective irreversible small-molecule inhibitor of FGFR2 Characterizing Receptor Flexibility to Predict Mutations That Lead to Human Adaptation of Influenza Hemagglutinin Conclusion I’ve recently become very interested in molecular dynamics, or MD. Why…
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