A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations

نویسندگان

  • Florent Hédin
  • Krystel El Hage
  • Markus Meuwly
چکیده

The quality of atomistic simulations depends decisively on the accuracy of the underlying energy function (force field). Of particular importance for condensed-phase properties are nonbonded interactions, including the electrostatic and Lennard-Jones terms. Permanent atomic multipoles (MTPs) are an extension to common point-charge (PC) representations in atomistic simulations. MTPs are commonly determined from and fitted to an ab initio Electrostatic Potential (ESP), and Lennard-Jones (LJ) parameters are obtained from comparison of experimental and computed observables using molecular dynamics (MD) simulations. For this a set of thermodynamic observables such as density, heat of vaporization, and hydration free energy is chosen, to which the parametrization is fitted. The current work introduces a comprehensive computing environment (Fitting Wizard (FW)) for optimizing nonbonded interactions for atomistic force fields of different qualities. The FW supports fitting of standard PC-based force fields and more physically motivated multipolar (MTP) force fields. A broader study including 20 molecules ranging from N-methyl-acetamide and benzene to halogenated benzenes, phenols, anilines, and pyridines yields a root mean squared deviation for hydration free energies of 0.36 kcal/mol over a range of 8 kcal/mol. It is furthermore shown that PC-based force fields are not necessarily inferior compared to MTP parametrizations depending on the molecule considered.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were determined by fitting to rotational energy profiles obtained ...

متن کامل

Coarse graining of nonbonded inter-particle potentials using automatic simplex optimization to fit structural properties

We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered in molecular dynamics simulations is reduced while conserving as many properties of the original substance as possible. We address the problem of finding nonb...

متن کامل

Determination of BKW Equation of State Parameters via Measurement of the Detonation Velocity in Condensed Explosives

An optical system has been redesigned and used to measure detonation velocity as a function of condensed explosive density for RDX, HMX, PETN. These measurements are then used to determine and fine tune parameters appearing in the BKW (Beker-Kistiakowsky-Wilson) equation of state for gases at extremely high pressures. Steady state form of conservation equations along with the BKW state equation...

متن کامل

Determination of BKW Equation of State Parameters via Measurement of the Detonation Velocity in Condensed Explosives

An optical system has been redesigned and used to measure detonation velocity as a function of condensed explosive density for RDX, HMX, PETN. These measurements are then used to determine and fine tune parameters appearing in the BKW (Beker-Kistiakowsky-Wilson) equation of state for gases at extremely high pressures. Steady state form of conservation equations along with the BKW state equation...

متن کامل

An investigation of neutron direct damages at energies of 0.1-2 MeV on the DNA molecules with atomic structure deduced using Geant4 toolkit

This study proposes a method to estimate RBE of fast neutrons using Monte Carlo simulations. This approach is based on the combination of an atomic resolution DNA geometrical model and Monte Carlo simulations for tracking particles. Atomic positions were extracted from the Protein Data Bank. The GEANT4 code was used for tracking the secondary particles generated by fast neutrons during their in...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • Journal of chemical information and modeling

دوره 57 1  شماره 

صفحات  -

تاریخ انتشار 2016