Hello, so far i've come across lots of papers using conventional MD to study stability of protein-ligand binding after molecular docking. What i am curious is, could accelerated MD be used for this purpose as well?
Dear Chee,
There are more algorithms to enhance your MD, and nowadays, people are shifting to Enhanced sampling, umbrella sampling etc., from conventional MD. You can go through different algorithms and find better ones for yourself.
If you talking about the program speeding itself, there are options in the newer program/versions for speed simulations, for your computer performance GPU acceleration as pointed out by Rudy Richardson is the very best option, and as for you need altogether change to your inputs and performance, the umbrella and enhanced, as well as non-Boltzman speeding-statistical ensembles, as told by Shaban Ahmad, check these out:
htts://www.sciencedirect.com/topics/agricultural-and-biological-sciences/umbrella-sampling
Article Enhanced Conformational Sampling in Molecular Dynamics Simul...
DOI: 10.1021/ct1003059
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