Applications > charmm

Publications

Users of this package associated the following 12 publications with the XSEDE allocation/account under which they were running this software. Thus the publications may have come before or after the runs of this software, but the authors considered them to be related to the same line of research.

  • James C. Browne, Thomas Furlani (SUNY at Buffalo), Robert T. McLay, Robert L. DeLeon, Charng-Da Lu, Matthew D. Jones, Steve Gallo (SUNY at Buffalo), Amin Ghadersohi, Abani K. Patra, William Barth (University of Texas at Austin), John Hammond, (November2013) "Enabling comprehensive data-driven system management for large computational facilities", Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '13 Denver, CO, USA , 1-11. http://dx.doi.org/10.1145/2503210.2503230
  • Cheng Zhang (UTMB), Bernard Pettitt (UTMB), (April2014) "Computation of high-order virial coefficients in high-dimensional hard-sphere fluids by Mayer sampling", Molecular Physics 112/9-10, 1427-1447. http://www.tandfonline.com/doi/abs/10.1080/00268976.2014.904945
  • Justin A Lemkul, Alexey Savelyev, Alexander D MacKerell, (June2014) "Induced Polarization Influences the Fundamental Forces in DNA Base Flipping", The Journal of Physical Chemistry Letters 5 / 12, 2077-2083. http://dx.doi.org/10.1021/jz5009517
  • Jing Huang (University of Maryland, Baltimore), Alexander D. MacKerell, (2013) "CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data", Journal of Computational Chemistry 34 / 25, 2135-2145. http://dx.doi.org/10.1002/jcc.23354
  • Chuanying Chen (University of Texas Medical Branch), Bernard Pettitt (University of Texas Medical Branch), (2011) "The Binding Process of a Nonspecific Enzyme with DNA", Biophysical Journal 101 / 5, 1139-1147. http://dx.doi.org/10.1016/j.bpj.2011.07.016
  • Hironori Kokubo (University of Houston-Downtown), Char Hu (University of Houston-Downtown), Bernard Pettitt (University of Texas Medical Branch), (2011) "Peptide Conformational Preferences in Osmolyte Solutions: Transfer Free Energies of Decaalanine", Journal of the American Chemical Society 133 / 6, 1849-1858. http://dx.doi.org/10.1021/ja1078128
  • John S Perkyns (University of Texas Medical Branch), Gillian C Lynch (University of Texas Medical Branch), Jesse J Howard (University of Houston-Downtown), B Montgomery Pettitt (University of Texas Medical Branch), (2010) "Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories", The Journal of Chemical Physics 132 / 6, 064106. http://dx.doi.org/10.1063/1.3299277
  • Thomas Furlani (SUNY at Buffalo), Matthew D. Jones, Steve Gallo (SUNY at Buffalo), Andrew E. Bruno, Charng-Da Lu, Amin Ghadersohi, Ryan J. Gentner, Abani Patra, Robert L. DeLeon, Gregor von Laszewski, Fugang Wang, Ann Zimmerman, (2012) "Performance metrics and auditing framework using application kernels for high-performance computer systems", Concurrency and Computation: Practice and Experience 25 / 7, 918-931. http://dx.doi.org/10.1002/cpe.2871
  • Svetla Stoilova-McPhie, Gillian C Lynch (University of Texas Medical Branch), Steven Ludtke, Bernard Montgomery Pettitt (University of Texas Medical Branch), (2013) "Domain organization of membrane-bound factor VIII", Biopolymers undefined / undefined, n/a-n/a. http://dx.doi.org/10.1002/bip.22199
  • Christopher G. Myers, Bernard Montgomery Pettitt (University of Texas Medical Branch), (March2013) "Communication: Origin of the contributions to DNA structure in phages", The Journal of Chemical Physics 138 / 7, 071103. http://dx.doi.org/10.1063/1.4791708
  • Loredana Mereuta, Mahua Roy, Alina Asandei, Jong Kook Lee, Yoonkyung Park, Ioan Andricioaei, Tudor Luchian, (2014) "Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation", Scientific Reports 4 / undefined, . http://dx.doi.org/10.1038/srep03885
  • Daniel Barr (Utica College), Taiji Oashi (University of Maryland, Baltimore County), Kimberly Burkhard, Sarah Lucius, Ramin Samadani, Jun Zhang, Paul Shapiro, Alexander D. MacKerell, Jr. (University of Maryland, Baltimore County), Arjan van der Vaart (University of South Florida), (August2011) "Importance of Domain Closure for the Autoactivation of ERK2", Biochemistry 50 / 37, 8038-8048. http://dx.doi.org/10.1021/bi200503a