Replica-Exchange Molecular Dynamics (REMD) is a class of simulation techniques used to enhance sampling and comprehensively explore phase space of molecular dynamics simulations. Historically, REMD implementations have been tightly coupled to their parent Molecular Dynamics (MD) packages. As a result, methodological improvements to these techniques are difficult to translate across packages, and therefore remain siloed in. RepEx decouples Replica Exchange methods from the MD packages by providing an API that allows for MD engine agnosticity and user-defined exchange methods. We use the RepEx framework to perform Independence Sampling REMD on a biomolecular mixed system consisting of two ultrashort peptides: Diphenylalanine (FF) and Phenylalanine-Asparagine-Phenylalanine (FNF). REMD simulations are typically used in conformational studies on single proteins, but seldom to understand aggregation: a class of physical processes which are especially susceptible to kinetic traps. Independence Sampling REMD provides enhanced sampling and increases replica mobility that aids the systems in overcoming these kinetic traps. Thus, we apply the technique to the assembly of ultrashort peptides and explore the morphological diversity of the supramolecular structures.<br/>

RepEx: Scalable, flexible, and extensible replica exchange framework

Macromolecular Chemistry: The Second Century

[Author Benefits](https://scimeetings.acs.org/?utm_source=pubs_content_marketing&utm_medium=website&utm_campaign=0320_MCF_NPI_Launch_Spring_Homepage&ref=pubs_content_marketing)

[How to use SciMeetings](https://storage.googleapis.com/dl.morressier.com/acs/SciMeetings-ACSSpring2020-HowToGuide_M3020-Final.pdf)

[Frequently Asked Questions](https://storage.googleapis.com/dl.morressier.com/acs/SciMtng_ACSNMSp2020_FAQ_M3120_Final.pdf)

ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.