Three‐site and five‐site fixed‐charge water models compatible with AMOEBA force field

2020 ◽  
Vol 41 (10) ◽  
pp. 1034-1044 ◽  
Author(s):  
Cong Pan ◽  
Chengwen Liu ◽  
Junhui Peng ◽  
Pengyu Ren ◽  
Xuhui Huang
Keyword(s):  
Force Field ◽  
Fixed Charge ◽  
Water Models ◽  
Amoeba Force Field

scholarly journals A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2695 ◽  
Author(s):  
Gerhard König ◽  
Frank Pickard ◽  
Jing Huang ◽  
Walter Thiel ◽  
Alexander MacKerell ◽  
...  
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Reaction Rates ◽  
Fixed Charge ◽  
Free Energies ◽  
Solvent Interactions ◽  
Scale Free ◽  
Mechanical Methods ◽  
Water Models ◽  
Energy Simulations

Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree–Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard–Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute–solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.

scholarly journals Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

2013 ◽  
Vol 9 (9) ◽  
pp. 4046-4063 ◽  
Author(s):  
Yue Shi ◽  
Zhen Xia ◽  
Jiajing Zhang ◽  
Robert Best ◽  
Chuanjie Wu ◽  
...  
Keyword(s):  
Force Field ◽  
Amoeba Force Field

AMOEBA force field parameterization of the azabenzenes

2014 ◽  
Vol 134 (1) ◽  
Author(s):  
David Semrouni ◽  
Christopher J. Cramer ◽  
Laura Gagliardi
Keyword(s):  
Force Field ◽  
Force Field Parameterization ◽  
Amoeba Force Field

scholarly journals Polarizable Amoeba Force Field Metadynamics with Minimization Predicts Missing Protein Loops

2017 ◽  
Vol 112 (3) ◽  
pp. 55a
Author(s):  
Armin Avdic ◽  
Mallory R. Tollefson ◽  
Nicole Tatro ◽  
Stephen D. LuCore ◽  
Jacob M. Litman ◽  
...  
Keyword(s):  
Force Field ◽  
Amoeba Force Field ◽  
Protein Loops

Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models

2018 ◽  
Vol 58 (5) ◽  
pp. 1037-1052 ◽  
Author(s):  
Haiyang Zhang ◽  
Chunhua Yin ◽  
Yang Jiang ◽  
David van der Spoel
Keyword(s):  
Amino Acids ◽  
Force Field ◽  
Water Models ◽  
And Diffusion

scholarly journals Capturing the Influence of Solvent and Neighboring Residues in a Fixed-Charge Force Field for RNA

2020 ◽  
Vol 118 (3) ◽  
pp. 68a
Author(s):  
Chapin E. Cavender ◽  
Louis G. Smith ◽  
Alan Grossfield ◽  
David H. Mathews
Keyword(s):  
Force Field ◽  
Fixed Charge ◽  
Influence Of Solvent
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