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. 2011 Dec;138(6):571–580. doi: 10.1085/jgp.201110670

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© 2011 Pan et al.

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Figure 2. — Overall alchemical FEP/MD strategy for transforming an alanine into a phenylalanine. Transparent atoms do not interact with other atoms in the system. Red dashed lines indicate a set of four atoms whose dihedral angle is harmonically restrained. Details of the calculation are described in the section Alchemical FEP/MD simulation.