Are the following conditions true for simulating the molecular dynamics of an enzyme in the blood?

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Zhaoxi Sun

ph=7.4

temperature=310 K

water as solvent

Note that the molecular dynamics modelling normally cannot reach the enzyme-in-blood level, and approximated models are used.

Martin Klvana

Room temperature (298 K), although different from living human body temperature, will be also fine. Some people always simulate at 300 K because it is a nicely round number, and that is actually a very good argument.

It is a good practice in MD simulations of nonperiodic systems (such as sphere) to keep ionizable residues located far from the region of interest neutral.