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Computational Chemistry
Gordon Research Conference

Accuracy and Sampling Across Quantum Chemistry and Molecular Modeling

Dates

July 20-25, 2014

Location

Mount Snow
West Dover, VT

Organizers

Chair:
Jay W. Ponder

Vice Chair:
Adrian J. Mulholland

Meeting Description

The 2014 Gordon Conference on Computational Chemistry will present a range of cutting-edge methodological developments and applications emphasizing the interplay of model accuracy and ability to sample the underlying physical system. The meeting has traditionally covered both quantum chemistry and classical force field-based modeling. The 2014 conference will attempt to compare and contrast techniques from both of these worlds when applied to a common application area. Sessions will highlight the tradeoffs and opportunities involved in selecting a method to correctly reproduce critical aspects of a system while remaining efficient enough to allow computation of a precise answer. Talks will be balanced between the traditional Conference focus on new methodology, and state-of-the-art applications. Some of the application topics expected to be covered include: sampling for free energy computations, modeling and prediction of pKa values, community-based distributed computing in computational chemistry, NMR-based calculations. The 2014 conference will adhere to the traditional GRC format with talks and posters focusing on new, unpublished work. Extensive time will be allocated for discussion and poster sessions to enable attendees to show and discuss their work. Overall, the goal of the conference is to bring together leading scientists from industry, academia and government to delineate future challenges in the interdisciplinary area of computational chemistry. Also, the conference will be paired with the first-ever Computational Chemistry Gordon Research Seminar, which will allow younger scientists to present their research and be mentored by established scientists in the field.

Related Meeting

This GRC was held in conjunction with the "Computational Chemistry" Gordon Research Seminar (GRS). Refer to the associated GRS program page for more information.

Contributors

Meeting Program

SUNDAY
2:00 pm - 9:00 pmArrival and Check-in
6:00 pmDinner
7:30 pm - 7:40 pmWelcome / Introductory Comments by GRC Site Staff
7:40 pm - 9:30 pmThe Future of Molecular Simulation and Quantum Chemistry
Discussion Leader: Jay Ponder (Washington University)
7:40 pm - 8:25 pmBill Jorgensen (Yale University)
"Free Energy Perturbation-Guided Lead Optimization"
8:25 pm - 8:35 pmDiscussion
8:35 pm - 9:20 pmPeter Gill (Australian National University)
"The Future of Quantum Chemistry"
9:20 pm - 9:30 pmDiscussion
MONDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmAccurate Free Energy Calculations
Discussion Leader: Pengyu Ren (University of Texas, Austin)
9:00 am - 9:35 amPengyu Ren (University of Texas, Austin)
"Free Energy Calculations: Methods and Applications"
9:35 am - 9:45 amDiscussion
9:45 am - 10:20 amJ.C. Gumbart (Georgia Institute of Technology)
"Exploring the Complex Free Energy Landscape of Helix Formation"
10:20 am - 10:30 amDiscussion
10:30 amCoffee Break
11:00 am - 11:35 amWei Yang (Florida State University)
"Orthogonal Space Sampling Methods to Enable Quantitative Free Energy Simulations"
11:35 am - 11:45 amDiscussion
11:45 am - 12:20 pmCarol Post (Purdue University)
"Thermodynamic Calculations from MD"
12:20 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pmStatus of DFT and Other Low-Cost Wavefunction Methods
Discussion Leader: Gus Scuseria (Rice University)
7:30 pm - 8:00 pmGus Scuseria (Rice University)
"Status of DFT and Recent Progress in Low-Polynomial Cost Wavefunction Methods"
8:00 pm - 8:10 pmDiscussion
8:10 pm - 8:40 pmDon Truhlar (University of Minnesota)
"Recent Advances in Incorporating Quantum Effects into Dynamics"
8:40 pm - 8:50 pmDiscussion
8:50 pm - 9:20 pmStefan Grimme (University of Bonn)
"Density Functional Theory for Supramolecular Systems"
9:20 pm - 9:30 pmDiscussion
TUESDAY
7:30 am - 8:30 amBreakfast
8:30 amGroup Photo
9:00 am - 12:30 pmNMR-Related Calculations
Discussion Leader: Dave Case (Rutgers University)
9:00 am - 9:35 amDave Case (Rutgers University)
"Quantum Fragmentation Approach to Computing Chemical Shifts in Biomolecules"
9:35 am - 9:45 amDiscussion
9:45 am - 10:20 amTeresa Carlomagno (EMBL, Heidelberg)
"Experiment Meets Computation: An NMR-Based Drug Design Approach"
10:20 am - 10:30 amDiscussion
10:30 amCoffee Break
11:00 am - 11:35 amRobert Best (NIDDK, National Institutes of Health)
"NMR Data as an Aid to Force Field Development"
11:35 am - 11:45 amDiscussion
11:45 am - 12:20 pmDoug Turner (University of Rochester)
"NMR Studies of Oligonucleotides as Benchmarks for RNA Force Fields"
12:20 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pmModeling of Protein pKa Values
Discussion Leader: Charlie Brooks (University of Michigan)
7:30 pm - 8:00 pmCharlie Brooks (University of Michigan)
"Constant pH Simulations: Exploring Membrane-Bound Proteins and Virus Maturation"
8:00 pm - 8:10 pmDiscussion
8:10 pm - 8:40 pmJens Nielsen (Novozymes, Copenhagen)
"Electrostatic Field Propagation: Experiments and Calculations"
8:40 pm - 8:50 pmDiscussion
8:50 pm - 9:20 pmJena Shen (University of Maryland, Baltimore)
"Recent Development and Application of All-Atom Constant pH Molecular Dynamics"
9:20 pm - 9:30 pmDiscussion
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmModeling Biomolecule-Membrane Interactions
Discussion Leader: Benoit Roux (University of Chicago)
9:00 am - 9:35 amBenoit Roux (University of Chicago)
"Biomolecule-Membrane Interactions: What Can Be Learned from Polarizable Force Fields?"
9:35 am - 9:45 amDiscussion
9:45 am - 10:20 amAlan Grossfield (University of Rochester Medical Center)
"Insights into G-Protein Coupled Receptors from Simulations at Multiple Resolutions"
10:20 am - 10:30 amDiscussion
10:30 amCoffee Break
11:00 am - 11:35 amYi Wang (The Chinese University of Hong Kong)
"Free Energy Calculation of Nanodiamond-Membrane Association: The Impact of Shape and Surface Chemistry"
11:35 am - 11:45 amDiscussion
11:45 am - 12:20 pmCarmen Domene (King's College, London)
"Studies of Ion Conduction Through Cell Membranes Using Free Energy Methods"
12:20 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:00 pm - 7:30 pmBusiness Meeting
Nominations for the Next Vice Chair; Fill in Conference Evaluation Forms; Discuss Future Site and Scheduling Preferences; Election of the Next Vice Chair
7:30 pm - 9:30 pmCommunity-Assisted Distributed Computing
Discussion Leader: Vijay Pande (Stanford University)
7:30 pm - 8:00 pmVijay Pande (Stanford University)
"Folding@Home: Using Markov State Models and Milliseconds of Molecular Dynamics to Simulate the Long Timescale Dynamics of Biomolecules"
8:00 pm - 8:10 pmDiscussion
8:10 pm - 8:40 pmGianni De Fabritiis (Universitat Pompeu Fabra)
"High-Throughput Molecular Dynamics"
8:40 pm - 8:50 pmDiscussion
8:50 pm - 9:20 pmRhiju Das (Stanford University)
"RNA Design Rules from a Massive Open Laboratory"
9:20 pm - 9:30 pmDiscussion
THURSDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmMethods for Treatment of Transition Metals
Discussion Leader: Clark Landis (University of Wisconsin)
9:00 am - 9:35 amClark Landis (University of Wisconsin)
"Valence Bond-like Descriptions of Transition Metal Complexes, Jahn-Teller Effects and Empirical Valence Bond Force Fields"
9:35 am - 9:45 amDiscussion
9:45 am - 10:20 amAngela Wilson (University of North Texas)
"Towards Quantum Chemical Accuracy for Transition Metal Species"
10:20 am - 10:30 amDiscussion
10:30 amCoffee Break
11:00 am - 11:35 amRob Deeth (University of Warwick)
"Transition Metal Force Fields with Explicit d-Electron Effects"
11:35 am - 11:45 amDiscussion
11:45 am - 12:20 pmLaura Gagliardi (University of Minnesota)
"Multiconfigurational Pair Density Functional Theory for Transition Metal Containing Systems"
12:20 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pmCoarse Grained and Multi-Scale Modeling
Discussion Leader: Cecilia Clementi (Rice University)
7:30 pm - 8:00 pmCecilia Clementi (Rice University)
"Multiscale Characterization of the Photocycle of Photoactive Yellow Protein"
8:00 pm - 8:10 pmDiscussion
8:10 pm - 8:40 pmSiewert-Jan Marrink (University of Groningen)
"Adaptive Resolution Simulations Using the Martini Force Field"
8:40 pm - 8:50 pmDiscussion
8:50 pm - 9:20 pmChristian Holm (Universität Stuttgart)
"Modelling of Ionic Liquids Across Scales"
9:20 pm - 9:30 pmDiscussion
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDeparture
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