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. Author manuscript; available in PMC: 2017 Jun 5.
Published in final edited form as: Enzymes. 2016 Mar 28;39:293–323. doi: 10.1016/bs.enz.2016.02.002

Fig. 10.

Fig. 10

Molecular dynamics protocol. Flow chart describing the protocol used to perform the all-atom MD simulations. Programs LEaP, SANDER, PMEMD, and PTRAJ are modules in the AMBER simulation package [84].