Journal
MOLECULAR SIMULATION
Volume 44, Issue 13-14, Pages 1062-1081Publisher
TAYLOR & FRANCIS LTD
DOI: 10.1080/08927022.2018.1475741
Keywords
Free energy protocol design; multi-scale simulations; convergence properties
Funding
- National Institutes of Health [GM107485, S10OD012346]
- Max Planck Society
- National Science Foundation [ACI-1548562, OCI-1053575]
- NATIONAL HEART, LUNG, AND BLOOD INSTITUTE [ZIAHL001051] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM107485] Funding Source: NIH RePORTER
Ask authors/readers for more resources
In this work, we employ simple model systems to evaluate the relative performance of two of the most important free energy methods: The Zwanzig equation (also known as Free energy perturbation') and Bennett's acceptance ratio method (BAR). Although our examples should be transferable to other kinds of free energy simulations, we focus on applications of multi-scale free energy simulations. Such calculations are especially complex, since they connect two different levels of theory with very different requirements in terms of speed, accuracy, sampling and parallelisability. We try to reconcile all those different factors by developing some simple criteria to guide the early stages of the development of a free energy protocol. This is accomplished by quantifying how many intermediate steps and how many potential energy evaluations are necessary in order to reach a certain level of convergence.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available