> > >> would you please tell me for compare dynamic peptide what time for MD >> is enough by gromacs?generally. > > You can take your 20 ns simulation, and divide it into 2-4 parts, each 10 (or 5) ns long. Then, calculate the property you are interested in for each part seperately. If 20 ns is more then enought, then the difference between the parts should be minimal. Another option is to calculate the variance of the propery you are calculating, vs. time.
--Omer.
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