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. Author manuscript; available in PMC: 2015 Jan 15.
Published in final edited form as: J Comput Chem. 2013 Oct 9;35(2):95–108. doi: 10.1002/jcc.23444

Figure 4.

Figure 4

Energy conservation during constant energy QM/MM MD simulations of N-methylacetamide (left) and alanine dipeptide (right) in a droplet of 408 and 403 SPC/Fw water molecules, respectively, with electronic embedding at 300 K using a time step of 0.5 fs. The QM region is highlighted and consists of the entire N-methylacetamide molecule but only part of alanine dipeptide with the QM/MM boundary crossing covalent bonds such that peptide bonds are left intact. Hydrogen link atoms are used to saturate dangling bonds in the QM region.