Implementing dimer metadynamics using gromacs

Journal of Computational Chemistry - Tập 39 Số 25 - Trang 2126-2132 - 2018
M. Nava1
1Department of Chemistry and Applied Biosciences ETH Zurich, and Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13 6900 Lugano Switzerland

Tóm tắt

We develop a Gromacs implementation of dimer metadynamics (DM) (JCTC 13, 425 [2017]) for enhanced sampling through artificial delocalization effects. This implementation is based entirely on a Plumed collective variable developed for this purpose, the fine tuning of Gromacs input parameters, modified forcefields and custom nonbonded interactions. We demonstrate this implementation on alanine dipeptide in vacuum and in water, and on the 12‐residue alanine polypeptide in water and compare the results with a standard multiple‐replica technique such as parallel tempering. In all the considered cases, this comparison is consistent and the results with DM are smoother and require shorter simulations, thus proving the consistency and effectiveness of this Gromacs implementation. © 2018 Wiley Periodicals, Inc.

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Journal of Computational Chemistry

Tập 39 Số 25

2126-2132

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