Dummy Atoms in Alchemical Free Energy Calculations.

ABSTRACT: In calculations of relative free energy differences, the number of atoms of the initial and final states is rarely the same. This necessitates the introduction of dummy atoms. These placeholders interact with the physical system only by bonded energy terms. We investigate the conditions necessary so that the presence of dummy atoms does not influence the result of a relative free energy calculation. On the one hand, one has to ensure that dummy atoms only give a multiplicative contribution to the partition function so that their contribution cancels from double-free energy differences. On the other hand, the bonded terms used to attach a dummy atom (or group of dummy atoms) to the physical system have to maintain it in a well-defined position and orientation relative to the physical system

SUBMITTER: Fleck M 

PROVIDER: S-EPMC8280730 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature