Force fieldsMOF materialsNegative thermal expansionPower spectraSelf-diffusion of guestsAn all-atom force field is developed for metal organic frameworks Zn 4 O(RCO2) 6 by fitting to quantum mechanics data. Molecular simulations are conducted to validate the force field by calculating thermal ...
The parametrization protocol is consistent with that employed for the existing CHARMM protein, nucleic acid, and lipid force fields. Thus, the present force field can be applied to investigate not only carbohydrates alone but also in interaction with these other important biomolecules....
The newly developed parameters allow for the modeling of linear, branched, and cyclic pyranose/furanose polysaccharides both alone and in heterogeneous systems including proteins, nucleic acids, and/or lipids when combined with existing additive CHARMM biomolecular force fields. 展开 ...
differencesforthenon-polarizableforcefieldsaremainlyin choicesonthenumbersofinteraction sites and the origin and extent of testing of the parameters in the energy expressions. Our efforts, as embodied in the development of the TIP3P and TIP4P models for water ...
The performance of several all-atom force fields for alkanes is compared and evaluated. Configurational-bias Monte Carlo simulations in the Gibbs ensemble were carried out to calculate the vaporliquid phase equilibria for methane, ethane, n-butane, n-pentane, and n-octane. The Williams, OPLS-AA...
All-atom (AA) or the united-atom (UA) force fields will be chosen because of the demand for more exact results or the lower computational cost, respectively. In order to make a systematic comparison of the two force fields, molecular simulations for four kinds of acyclic guanidinium-based ...
Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055): 517520]. These results indicate that modern force fields can reproduce the energy surface near the...
Development and Testing of the OPLS All-Atom Force Fields on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118,... C Evenhuis,TJ Martnez - 《Journal of Chemical Physics》 被引量: 0发表: 2011年 Multiscale Coarse-Graining of Ionic Liquids ? Development...
DMD simulations of simplified protein models with structure-based force fields have been used in previous studies of protein folding and aggregation (Dokholyan et al., 2000). Despite the simplicity of the protein models used, the DMD simulations show strikingly predictive power in uncovering the un...
CHARMM General Force Field (CGenFF): A Force Field for Drug-like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields. J. ... A.,V.,Morozov,... - 《Proceedings of the National Academy of Sciences of the United States of America》 被引量: 433发表: 2004年 Pote...