CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.
Wonmuk HwangSteven L AustinArnaud BlondelEric D BoittierStefan BoreschMatthias BuckJoshua BucknerAmedeo CaflischHao-Ting ChangXi ChengYeol Kyo ChoiJhih-Wei ChuMichael F CrowleyQiang CuiAna DamjanovicYuqing DengMichael DevereuxXinqiang DingMichael F FeigJiali GaoDavid R GlowackiJames E GonzalesMehdi Bagerhi HamanehEdward D HarderRyan L HayesJing HuangYandong HuangPhillip S HudsonWonpil ImShahidul M IslamWei JiangMichael R JonesSilvan KäserFiona L KearnsNathan R KernJeffery B KlaudaThemis LazaridisJinhyuk LeeJustin A LemkulXiaorong LiuYun Lyna LuoAlexander D MacKerellDan Thomas MajorMarkus MeuwlyKwangho NamLennart NilssonVictor OvchinnikovEmanuele PaciSoohyung ParkRichard W PastorAmanda R PittmanCarol Beth PostSamarjeet PrasadJingzhi PuJohn Z H ZhangThenmalarchelvi RathinavelanDaniel R RoeBenoı T RouxChristopher N RowleyJana ShenAndrew C SimmonettAlexander J SodtKai TöpferMeenu UpadhyayArjan van der VaartLuis Itza Vazquez-SalazarRichard M VenableLuke C WarrensfordH Lee WoodcockYujin WuCharles L Brooks IiiBernard R BrooksMartin KarplusPublished in: The journal of physical chemistry. B (2024)
Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.