Hi all,
I am learning a lot of things about the computational biology for the first time. I was curious, with the current technology, what is the possible simulation time range for a research in computational biology using commercial force fields such as AMBER, GROMACS, CHARMM etc? Can we go more than ns without harming the results?
Thanks!
What is "possible" is limited only by the quality of the hardware and software (and how much patience you have for waiting on the results). Modern simulations often go well into the microsecond range pretty easily.
The better question is what is necessary to answer the question(s) at hand, and sampling is a general concern. A single, microsecond-length simulation may be less valuable than, say, 10 x 100-ns simulations, but of course that again depends on the purpose(s) of the simulation. Long simulations have exposed the fact that conformations often get trapped in local minima for long periods of time. This can be circumvented with enhanced sampling techniques or by simply running many more simulations from different starting conformations and/or initial (random) velocities.
Dear Cece Hong,
Please go through this link; https://www.researchgate.net/post/What_is_the_optimum_time_in_ns_to_do_MD_simulation_for_drug_design
What is "possible" is limited only by the quality of the hardware and software (and how much patience you have for waiting on the results). Modern simulations often go well into the microsecond range pretty easily.
The better question is what is necessary to answer the question(s) at hand, and sampling is a general concern. A single, microsecond-length simulation may be less valuable than, say, 10 x 100-ns simulations, but of course that again depends on the purpose(s) of the simulation. Long simulations have exposed the fact that conformations often get trapped in local minima for long periods of time. This can be circumvented with enhanced sampling techniques or by simply running many more simulations from different starting conformations and/or initial (random) velocities.
Please consider Justin's answer that correct. However, my quick & dirty contribution is 200 msec.
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