Paper Citing NAMD - Abstract
Carlotto, Silvia; Zerbetto, Mirco
Computational Study of Environmental Effects on Torsional Free Energy Surface of N-Acetyl-N '-methyl-L-alanylamide Dipeptide
JOURNAL OF CHEMICAL EDUCATION, 91:96-102, JAN 2014
We propose an articulated computational experiment in which both quantum mechanics (QM) and molecular mechanics (MM) methods are employed to investigate environment effects on the free energy surface for the backbone dihedral angles rotation of the small dipeptide N-acetyl-N'-methyl-L-alanylamide. This computation exercise is appropriate for an upper-level physical chemistry course. The purposes are (0 to show the importance of solvent effects on the free energy surface of molecules in solution and (ii) to compare different computational chemistry tools in terms of computation complexity versus detail of information obtained from calculus. The QM section is divided in three parts: in vacuo, implicit solvent, and explicit solvent calculations. Similarly, also the MM section is divided in three parts: molecular mechanics, molecular dynamics, and adaptive biasing force molecular dynamics. QM and MM sections can be proposed by the instructor as different and complementary parts of the experiment or as independent QM or MM class lessons. Together, the two sections can be used to set up a computational chemistry laboratory exercise targeted to the study of solvent effects on molecular properties.
