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In our latest experiments, we did a molecular docking simulation by using "CHARMm" forcefield and it went well. However when we were doing molecular dynamics simulation by using an exact same...
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Our colleague suggests that, by bought the $1000 VGA card to our computer, our simulation would run incredibly faster, and can easily achieve 100 ns MD simulation in less than a week even though...
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So far we're using MD simulation to get RMSD result of the protein-ligand complex and see which one is the best. So far we didn't have the tutorial for doing Thermodynamic Integration MD...
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