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arXiv · 1702.01770

PHAST: Protein-like heteropolymer analysis by statistical thermodynamics

Rafael B. Frigori
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Abstract

PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for proteins. The outcome data can be straightforwardly analyzed within its microcanonical Statistical Thermodynamics module, which allows for computing the entropy, caloric curve, specific heat and free energies. As a case study, we investigate the aggregation of heteropolymers bioinspired on $A\beta_{25-33}$ fragments and their cross-seeding with $IAPP_{20-29}$ isoforms. Excellent parallel scaling is observed, even under numerically difficult first-order like phase transitions, which are properly described by the built-in fully reconfigurable force fields. Still, the package is free and open source, this shall motivate users to readily adapt it to specific purposes.

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BibTeXRIS

Rafael B. Frigori. 2017-02-06. PHAST: Protein-like heteropolymer analysis by statistical thermodynamics. https://doi.org/10.1016/j.cpc.2017.01.021

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