Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

被引:33
作者
Beauchamp, Kyle A. [1 ]
Behr, Julie M. [2 ]
Rustenburg, Arien S. [3 ]
Bayly, Christopher I. [4 ]
Kroenlein, Kenneth [5 ]
Chodera, John D. [1 ]
机构
[1] Mem Sloan Kettering Canc Ctr, Sloan Kettering Inst, Computat Biol Program, New York, NY 10065 USA
[2] Weill Cornell Med Coll, Triinst Program Computat Biol & Med, New York, NY 10065 USA
[3] Weill Cornell Med Coll, Grad Program Physiol Biophys & Syst Biol, New York, NY 10065 USA
[4] OpenEye Sci Software Inc, Santa Fe, NM 87508 USA
[5] NIST, Thermodynam Res Ctr, Boulder, CO 80305 USA
关键词
THERMOCHEMICAL PROPERTY DATA; XML-BASED APPROACH; MOLECULAR-DYNAMICS; EFFICIENT GENERATION; POTENTIAL FUNCTIONS; ORGANIC LIQUIDS; CONDENSED-PHASE; AM1-BCC MODEL; DATA SET; POLARIZATION;
D O I
10.1021/acs.jpcb.5b06703
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical 0 properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.
引用
收藏
页码:12912 / 12920
页数:9
相关论文
共 64 条
[51]   Temperature and pressure dependence of the AMOEBA water model [J].
Ren, PY ;
Ponder, JW .
JOURNAL OF PHYSICAL CHEMISTRY B, 2004, 108 (35) :13427-13437
[52]   Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald [J].
Salomon-Ferrer, Romelia ;
Goetz, Andreas W. ;
Poole, Duncan ;
Le Grand, Scott ;
Walker, Ross C. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2013, 9 (09) :3878-3888
[53]   Statistically optimal analysis of samples from multiple equilibrium states [J].
Shirts, Michael R. ;
Chodera, John D. .
JOURNAL OF CHEMICAL PHYSICS, 2008, 129 (12)
[54]   Accurate molecular polarizabilities based on continuum electrostatics [J].
Truchon, Jean-Francois ;
Nicholls, Anthony ;
Iftimie, Radu I. ;
Roux, Benoit ;
Bayly, Christopher I. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2008, 4 (09) :1480-1493
[55]   Using Electronic Polarization From the Internal Continuum (EPIC) for Intermolecular Interactions [J].
Truchon, Jean-Francois ;
Nicholl's, Anthony ;
Grant, J. Andrew ;
Iftimie, Radu I. ;
Roux, Benoit ;
Bayly, Christopher I. .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2010, 31 (04) :811-824
[56]   Integrated Continuum Dielectric Approaches To Treat Molecular Polarizability and the Condensed Phase: Refractive Index and Implicit Solvation [J].
Truchon, Jean-Francois ;
Nicholls, Anthony ;
Roux, Benoit ;
Iftimie, Radu I. ;
Bayly, Christopher I. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2009, 5 (07) :1785-1802
[57]   BioMagResBank [J].
Ulrich, Eldon L. ;
Akutsu, Hideo ;
Doreleijers, Jurgen F. ;
Harano, Yoko ;
Ioannidis, Yannis E. ;
Lin, Jundong ;
Livny, Miron ;
Mading, Steve ;
Maziuk, Dimitri ;
Miller, Zachary ;
Nakatani, Eiichi ;
Schulte, Christopher F. ;
Tolmie, David E. ;
Wenger, R. Kent ;
Yao, Hongyang ;
Markley, John L. .
NUCLEIC ACIDS RESEARCH, 2008, 36 :D402-D408
[58]   Time-Averaged Distributions of Solute and Solvent Motions: Exploring Proton Wires of GFP and PfM2DH [J].
Velez-Vega, Camilo ;
McKay, Daniel J. J. ;
Aravamuthan, Vibhas ;
Pearlstein, Robert ;
Duca, Jose S. .
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2014, 54 (12) :3344-3361
[59]   Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39) [J].
Voelz, Vincent A. ;
Bowman, Gregory R. ;
Beauchamp, Kyle ;
Pande, Vijay S. .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2010, 132 (05) :1526-+
[60]   Development and testing of a general amber force field [J].
Wang, JM ;
Wolf, RM ;
Caldwell, JW ;
Kollman, PA ;
Case, DA .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2004, 25 (09) :1157-1174