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@ARTICLE{Buslaev:827046,
      author       = {Buslaev, Pavel and Gordeliy, Valentin and Grudinin, Sergei
                      and Gushchin, Ivan},
      title        = {{P}rincipal {C}omponent {A}nalysis of {L}ipid {M}olecule
                      {C}onformational {C}hanges in {M}olecular {D}ynamics
                      {S}imulations},
      journal      = {Journal of chemical theory and computation},
      volume       = {12},
      number       = {3},
      issn         = {1549-9618},
      address      = {Washington, DC},
      reportid     = {FZJ-2017-01252},
      pages        = {1019-1028},
      year         = {2016},
      abstract     = {Molecular dynamics simulations of lipid bilayers are
                      ubiquitous nowadays. Usually, either global properties of
                      the bilayer or some particular characteristics of each lipid
                      molecule are evaluated in such simulations, but the
                      structural properties of the molecules as a whole are rarely
                      studied. Here, we show how a comprehensive quantitative
                      description of conformational space and dynamics of a single
                      lipid molecule can be achieved via the principal component
                      analysis (PCA). We illustrate the approach by analyzing and
                      comparing simulations of DOPC bilayers obtained using eight
                      different force fields: all-atom generalized AMBER,
                      CHARMM27, CHARMM36, Lipid14, and Slipids and united-atom
                      Berger, GROMOS43A1-S3, and GROMOS54A7. Similarly to
                      proteins, most of the structural variance of a lipid
                      molecule can be described by only a few principal
                      components. These major components are similar in different
                      simulations, although there are notable distinctions between
                      the older and newer force fields and between the all-atom
                      and united-atom force fields. The DOPC molecules in the
                      simulations generally equilibrate on the time scales of tens
                      to hundreds of nanoseconds. The equilibration is the slowest
                      in the GAFF simulation and the fastest in the Slipids
                      simulation. Somewhat unexpectedly, the equilibration in the
                      united-atom force fields is generally slower than in the
                      all-atom force fields. Overall, there is a clear separation
                      between the more variable previous generation force fields
                      and significantly more similar new generation force fields
                      (CHARMM36, Lipid14, Slipids). We expect that the presented
                      approaches will be useful for quantitative analysis of
                      conformations and dynamics of individual lipid molecules in
                      other simulations of lipid bilayers.},
      cin          = {ICS-6},
      ddc          = {540},
      cid          = {I:(DE-Juel1)ICS-6-20110106},
      pnm          = {551 - Functional Macromolecules and Complexes (POF3-551)},
      pid          = {G:(DE-HGF)POF3-551},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000371852300012},
      pubmed       = {pmid:26765212},
      doi          = {10.1021/acs.jctc.5b01106},
      url          = {https://juser.fz-juelich.de/record/827046},
}