Hi everyone,
I just carried out a series of simulation steps, including an energy
minimization for 1000 steps, a heating for 50ps from 0k to 300k, a density
equilibration for 50ps, a constant-pressure equilibration for 500ps, and a
production MD for 2ns. Before this, I also added a 10 angstrom buffer of
water around the system in addition to the already defined crystallographic
waters.
The question is that if there is any basis for selecting these step sizes
(1000 steps, 50ps, etc.) and boundary condition artifacts?
Another question is for the time to do the production MD. It is said that,
in such short time simulation (2ns), most of the structures we observed are
very similar to the starting structure. As I started the simulation from a
relative stable structure (Crystal structure by X-ray diffraction), how
long should I perform the simulation? Is there any benchmark?
Thanks very much.
--
Regards,
ZOU, Bin
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Received on Thu Mar 17 2016 - 23:00:03 PDT
