How much nano second time study is required for study molecular dynamics in protein-protein complex to publish in journal?
There is no answer to this question that anyone can give you. A simulation must be long enough to converge the dynamics of interest and exhibit equilibrium sampling. Everything depends on what you're trying to study, and depends again on the size of the system. For example, two small proteins with only one domain could perhaps be studied in a matter of tens or hundreds of nanoseconds. Complexes of multi-domain proteins may require microseconds or milliseconds depending on the time scale of domain motion.
And the goal should not be simply to publish. The goal should be to do a robust simulation that has reliable outcomes.
There is no answer to this question that anyone can give you. A simulation must be long enough to converge the dynamics of interest and exhibit equilibrium sampling. Everything depends on what you're trying to study, and depends again on the size of the system. For example, two small proteins with only one domain could perhaps be studied in a matter of tens or hundreds of nanoseconds. Complexes of multi-domain proteins may require microseconds or milliseconds depending on the time scale of domain motion.
And the goal should not be simply to publish. The goal should be to do a robust simulation that has reliable outcomes.
Perfect answer Justin Lemkul .
Always have a goal before starting the dynamic simulation and run until you get what you want, if not extend it.
If you are really unsure, the attached image can give you some idea about it. The figure is part of the manuscript ( Article Reaching biological timescales with all-atom molecular dynam...
) that you can give a read.All the best. Cheers.
Depends on the system which you are studying. Mostly, they will be 1 ns to 1 ms in time-level.
Thank you Justin Lemkul and Pallab Kumar Borah , for your valuable suggestion.
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