Automated free-energy calculation from atomistic simulations

نویسندگان

چکیده

We devise automated workflows for the calculation of Helmholtz and Gibbs free energies their temperature pressure dependence provide corresponding computational tools. employ non-equilibrium thermodynamics evaluating energy solid liquid phases at a given reversible scaling computing over wide range temperatures, including direct integration $P$-$T$ coexistence lines. By changing chemistry interatomic potential, alchemical upscaling calculations are possible. Several examples illustrate accuracy efficiency our implementation.

برای دانلود باید عضویت طلایی داشته باشید

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

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Free-energy landscape of protein oligomerization from atomistic simulations.

In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most e...

متن کامل

Calculation of free energy changes due to mutations from alchemical free energy simulations

How a mutation a®ects the binding free energy of a ligand is a fundamental problem in molecular biology/biochemistry with many applications in pharmacology and biotechnology, e.g. design of drugs and enzymes. Free energy change due to a mutation can be determined most accurately by performing alchemical free energy calculations in molecular dynamics (MD) simulations. Here we discuss the necessa...

متن کامل

The mold integration method for the calculation of the crystal-fluid interfacial free energy from simulations.

The interfacial free energy between a crystal and a fluid, γcf, is a highly relevant parameter in phenomena such as wetting or crystal nucleation and growth. Due to the difficulty of measuring γcf experimentally, computer simulations are often used to study the crystal-fluid interface. Here, we present a novel simulation methodology for the calculation of γcf. The methodology consists in using ...

متن کامل

Free Energy Calculation from Steered Molecular Dynamics Simulations Using Jarzynski’s Equality

Jarzynski’s equality is applied to free energy calculations from steered molecular dynamics simulations of biomolecules. The helix-coil transition of deca-alanine in vacuum is used as an example. With about ten trajectories sampled, the second order cumulant expansion, among the various averaging schemes examined, yields the most accurate estimates. We compare umbrella sampling and the present ...

متن کامل

Temperature dependence of the surface free energy and surface stress: An atomistic calculation for Cu(110)

We propose a method to deduce the free energies ! and stresses " of plane surfaces and solid-liquid interfaces in elemental systems from atomistic simulations involving nonhydrostatically stressed solid phases. The method is applied to compute the temperature dependencies of ! and " for the !110" Cu surface using Monte Carlo simulations with an embedded-atom potential. Both quantities decrease ...

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

ژورنال

عنوان ژورنال: Physical Review Materials

سال: 2021

ISSN: ['2476-0455', '2475-9953']

DOI: https://doi.org/10.1103/physrevmaterials.5.103801