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Abstract: The absolute free energy - or partition function, equivalently - of amolecule can be estimated computationally using a suitable reference system.Here, we demonstrate a practical method for staging such calculations bygrowing a molecule based on a series of fragments. Significant computer time issaved by pre-calculating fragment configurations and interactions for re-use ina variety of molecules. We employ such fragment libraries and interactiontables for amino acids and capping groups to estimate free energies for smallpeptides. Equilibrium ensembles for the molecules are generated at noadditional computational cost, and are used to check our results by comparisonto standard dynamics simulation.



Autor: Xin Zhang, Artem B. Mamonov, Daniel M. Zuckerman

Fuente: https://arxiv.org/







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