Biophysical Society 59th Annual Meeting Program Guide

794-P os B oard B574 IMPLEMENTATION OF REPLICA-EXCHANGE UMBRELLA SAMPLING TO THE DFTB+ SIMULATION PACKAGE. Shingo Ito , Yuko Okamoto, Stephan Irle 795-P os B oard B575 CHARMM GUI MEMBRANE BUILDER UPDATES. Xi Cheng , Yifei Qi, Jumin Lee, Sunhwan Jo, Wonpil Im 796-P os B oard B576 EXPERIMENTAL AND THEORETICAL APPROACHES TO THE STUDY OF PROBE DIFFUSION IN MACROMOLECULAR SOLUTIONS. Preston Donovan , Yasaman Chehreghanianzabi, Muruhan Rathinam, Silviya Zustiak 797-P os B oard B577 A COUPLED TWO-DIMENSIONAL MAIN CHAIN TORSIONAL POTENTIAL FOR PROTEIN DYNAMICS. Ya Gao, Yongxiu Li, John Z.H. Zhang, Ye Mei 798-P os B oard B578 MOLECULAR DYNAMICS SIMULATION OF PROTEIN CRYSTAL WITH POLARIZED PROTEIN-SPECIFIC CHARGE. Yongxiu Li, John Z.H. Zhang, Ye Mei 799-P os B oard B579 EXTENSION OF THE CHARMM GENERAL FORCE FIELD TO LINKED NITROGEN-CONTAINING HETREROAROMATIC RINGS. Lei Fang , Ignacio Soteras Gutiérrez, Kenno Vanommeslaeghe, Alexander D. MacKerell Jr. 800-P os B oard B580 PHASE DIAGRAM OF LIPID-CHOLESTEROL MIXTURE: COMPARISON BETWEEN DIFFERENT FORCE FIELDS. Fernando Favela-Rosales , César Millán-Pacheco, Humberto Saint- Martin, Mauricio D. Carbajal-Tinoco, Iván Ortega-Blake 801-P os B oard B581 NON-MARKOVIAN ANALYSES FOR EXTRACTING LONG- TIME BEHAVIOR FROM MOLECULAR SIMULATION TRAJECTORIES. Ernesto Suarez , Daniel M. Zuckerman 802-P os B oard B582 NEW DEVELOPMENTS IN THE COLLECTIVE VARIABLES MODULE: MORE FLEXIBLE, MORE INTERACTIVE. Giacomo Fiorin , Jérôme Hénin 803-P os B oard B583 PARAMETRIZATION OF HALOGEN BONDS IN THE CHARMM GENERAL FORCE FIELD. Ignacio Soteras Gutierrez 804-P os B oard B584 LOOS: A TOOL FOR MAKING NEW TOOLS FOR ANALYZING MOLECULAR SIMULATIONS. Tod D. Romo , Alan Grossfield 805-P os B oard B585 A SMOLUCHOWSKI EQUATION FOR FORCE-MODULATED CHEMISTRY IN SINGLE MOLECULE PULLING EXPERIMENTS. Gianmarc Grazioli , Ioan Andricioaei 806-P os B oard B586 CHARMM-GUI MARTINI MAKER FOR COARSE-GRAINED SIMULATIONS. Yifei Qi , Xi Cheng, Wonpil Im 807-P os B oard B587 NECESSITY OF HIGH PHYSICAL RESOLUTION IN THE DEVELOPMENT OF FLEXIBLE COARSE-GRAINED PROTEIN MODELS. ZhiGuang Jia , Jianhan Chen

782-P os B oard B562 ENHANCED CONFORMATIONAL SAMPLING OF

CARBOHYDRATES USING BIASING POTENTIAL AND SOLUTE TEMPERING REPLICA EXCHANGE: APPLICATION TO THE N-GLYCAN ON THE HIV GP120 ENVELOPE PROTEIN. Mingjun Yang , Jing Huang, Alexander D. MacKerell Jr. 783-P os B oard B563 DMD4B-HYDRA: TOWARD A NOVEL DISCRETE MOLECULAR DYNAMICS PROTEIN MODEL. Derya Meral , Brigita Urbanc 784-P os B oard B564 TETRAMOLECULAR PARALLEL G-QUADRUPLEX VALIDATION SET FOR MOLECULAR DYNAMICS SIMULATION WITH CHARMM 27 FORCE FIELD. Daniela Barragan, Marcos V. Becerra , Miguel A. Mendez 785-P os B oard B565 SAMBE: THE NEWWEBSERVER FOR PREDICTING THE EFFECT OF NSSNP ON THE PROTEIN-PROTEIN BINDING FREE ENERGY. Marharyta Petukh , Jacon Morrison, Minghui Li, Anna Panchenko, Emil Alexov 786-P os B oard B566 BIO.B-GEN: AN INITIAL SYSTEM GENERATOR FOR BIOLOGICAL MOLECULAR SIMULATIONS. Dmitri Rozmanov , Peter Tieleman 787-P os B oard B567 VALIDATION AND DEVELOPMENT OF THE FORCE FIELD PARAMETERS FOR DRUG AND DRUG-LIKE MOLECULES. Katarzyna B. Koziara , Martin Stroet, Alpeshkumar K. Malde, Alan E. Mark 788-P os B oard B568 international travel awardee A NOVEL METHOD FOR FORCE-FIELD CALIBRATION BASED ON MAXIMUM-LIKELIHOOD APPROACH AND THERMAL UNFOLDING DATA. Bartłomiej Zaborowski, Dawid Jagieła, Adam K. Sieradzan, Cezary R. Czaplewski, Anna Hałabis, Agnieszka Lewandowska, Wioletta Żmudzińska, Stanisław Ołdziej, Jozef A. Liwo 789-P os B oard B569 QUANTUM MECHANICAL MOLECULAR MECHANICAL CALCULATIONS USING AMOEBA FORCE FIELDS. Yihan Shao , Andrew Simmonett, Frank Pickard, Gerhard Koenig, Bernard Brooks 790-P os B oard B570 THE DO’S AND DO NOT’S OF A 100 MILLION ATOM MOLECULAR DYNAMICS SIMULATION. Abhishek Singharoy , Danielle Chandler, Jacob Durrant, Melih Sener, Rommie Amaro, Klaus Schulten 791-P os B oard B571 MINIMALLY-BIASED METADYNAMICS METHOD TO SAMPLE CONFORMATIONAL ENSEMBLES COMPATIBLE WITH EXPERIMENTAL MEASUREMENTS. Fabrizio Marinelli , José D. Faraldo-Gómez 792-P os B oard B572 EFFICIENT HIGH ACCURACY NON-BONDED INTERACTIONS IN THE CHARMM SIMULATION PACKAGE. Frank C. Pickard , Andrew Craig Simmonett, Bernard Rigoberto Brooks 793-P os B oard B573 TOWARDS A POLARIZABLE FORCE FIELD FOR RNA BASED ON THE CLASSICAL DRUDE OSCILLATOR. Justin A. Lemkul , Alexey Savelyev, Alexander D. MacKerell, Jr.

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Biophysical Society 59 th Annual Meeting, Baltimore, Maryland