Dear researchers,
I'm currently doing an ensemble-based virtual screening.
May I asked How many pico/nanoseconds should run for Molecular dynamics simulation of a protein?
Do the production run must be conducted for 100,000 ps time scale under constant temperature (300 K) and pressure (1 bar)?
Thanks a lot.
Actually it varies. At least you have to run the simulation for 50 ns (50,000 ps). If you do not get the desired interactions then you can increase the time duration to 100,000 ps to 200,000 ps.
Usually 100ns is recommended but now reviewers usually ask for more than 200ns or so.
This will need a lot of computational power and time to complete.
You can also check this previous discussion (https://www.researchgate.net/post/In-Molecular-dynamic-simulation-study-of-protein-protein-complex-how-much-nano-second-of-time-is-minimum-for-md-run-rmsd-and-rmsf)
Regards.
At least 100000 ps you have to run but now a days 200000-300000 ps is used for protein-ligand complex.
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