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Implementing Dimer Metadynamics Using Gromacs
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DOI：10.1002/jcc.25386.png)
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Abstract
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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. (C) 2018 Wiley Periodicals, Inc.
Keywords:
Gromacs
replica exchange
enhanced sampling
protein simulation
dimer metadynamics
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