Adaptively restrained molecular dynamics in LAMMPS
نویسندگان
چکیده
منابع مشابه
Adaptively Restrained Molecular Dynamics in LAMMPS
Adaptively Restrained Molecular Dynamics (ARMD) is a recently introduced particles simulation method that switches positional degrees of freedom on and off during simulation in order to speed up calculations. In the NVE ensemble, ARMD allows users to trade between precision and speed while, in the NVT ensemble, it makes it possible to compute statistical averages faster. Despite the conceptual ...
متن کاملAdaptively restrained particle simulations.
Interaction potentials used in particle simulations are typically written as a sum of terms which depend on just a few relative particle positions. Traditional simulation methods move all particles at each time step, and may thus spend a lot of time updating interparticle forces. In this Letter we introduce adaptively restrained particle simulations (ARPS) to speed up particle simulations by ad...
متن کاملImplementation of Green's function molecular dynamics: An extension to LAMMPS
The Green’s function molecular dynamics method, which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only the surface atoms, was implemented as an extension to an open source classical molecular dynamics simulation code LAMMPS. This was done in the style of fixes. The first fix, FixGFC, measures the elastic stiffne...
متن کاملExploring the Use of Adaptively Restrained Particles for Graphics Simulations
In this paper, we explore the use of Adaptively Restrained (AR) particles for graphics simulations. Contrary to previous methods, Adaptively Restrained Particle Simulations (ARPS) do not adapt time or space sampling, but rather switch the positional degrees of freedom of particles on and off, while letting their momenta evolve. Therefore, inter-particles forces do not have to be updated at each...
متن کاملProtein folding by restrained energy minimization and molecular dynamics.
Native-like folded conformations of bovine pancreatic trypsin inhibitor protein are calculated by searching for conformations with the lowest possible potential energy. Twenty-five random starting structures are subjected to soft-atom restrained energy minimization with respect to both the torsion angles and the atomic Cartesian co-ordinates. The restraints used to limit the search include the ...
متن کاملذخیره 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: Modelling and Simulation in Materials Science and Engineering
سال: 2017
ISSN: 0965-0393,1361-651X
DOI: 10.1088/1361-651x/aa7345