100,206 research outputs found
Computing the local pressure in molecular dynamics simulations
Computer simulations of inhomogeneous soft matter systems often require
accurate methods for computing the local pressure. We present a simple
derivation, based on the virial relation, of two equivalent expressions for the
local (atomistic) pressure in a molecular dynamics simulation. One of these
expressions, previously derived by other authors via a different route,
involves summation over interactions between particles within the region of
interest; the other involves summation over interactions across the boundary of
the region of interest. We illustrate our derivation using simulations of a
simple osmotic system; both expressions produce accurate results even when the
region of interest over which the pressure is measured is very small.Comment: 11 pages, 4 figure
Elastic constants from microscopic strain fluctuations
Fluctuations of the instantaneous local Lagrangian strain
, measured with respect to a static ``reference''
lattice, are used to obtain accurate estimates of the elastic constants of
model solids from atomistic computer simulations. The measured strains are
systematically coarse- grained by averaging them within subsystems (of size
) of a system (of total size ) in the canonical ensemble. Using a
simple finite size scaling theory we predict the behaviour of the fluctuations
as a function of and extract elastic
constants of the system {\em in the thermodynamic limit} at nonzero
temperature. Our method is simple to implement, efficient and general enough to
be able to handle a wide class of model systems including those with singular
potentials without any essential modification. We illustrate the technique by
computing isothermal elastic constants of the ``soft'' and the hard disk
triangular solids in two dimensions from molecular dynamics and Monte Carlo
simulations. We compare our results with those from earlier simulations and
density functional theory.Comment: 24 pages REVTEX, 10 .ps figures, version accepted for publication in
Physical Review
Multi-Architecture Monte-Carlo (MC) Simulation of Soft Coarse-Grained Polymeric Materials: SOft coarse grained Monte-carlo Acceleration (SOMA)
Multi-component polymer systems are important for the development of new
materials because of their ability to phase-separate or self-assemble into
nano-structures. The Single-Chain-in-Mean-Field (SCMF) algorithm in conjunction
with a soft, coarse-grained polymer model is an established technique to
investigate these soft-matter systems. Here we present an im- plementation of
this method: SOft coarse grained Monte-carlo Accelera- tion (SOMA). It is
suitable to simulate large system sizes with up to billions of particles, yet
versatile enough to study properties of different kinds of molecular
architectures and interactions. We achieve efficiency of the simulations
commissioning accelerators like GPUs on both workstations as well as
supercomputers. The implementa- tion remains flexible and maintainable because
of the implementation of the scientific programming language enhanced by
OpenACC pragmas for the accelerators. We present implementation details and
features of the program package, investigate the scalability of our
implementation SOMA, and discuss two applications, which cover system sizes
that are difficult to reach with other, common particle-based simulation
methods
Computational structure‐based drug design: Predicting target flexibility
The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing a competitive advantage in early phases of drug discovery. Medium and small companies with strong focus on computational chemistry are being created, some of them having introduced important leads in drug design pipelines. An important source for this success is the extraordinary development of faster and more efficient techniques for describing flexibility in three‐dimensional structural molecular modeling. At different levels, from docking techniques to atomistic molecular dynamics, conformational sampling between receptor and drug results in improved predictions, such as screening enrichment, discovery of transient cavities, etc. In this review article we perform an extensive analysis of these modeling techniques, dividing them into high and low throughput, and emphasizing in their application to drug design studies. We finalize the review with a section describing our Monte Carlo method, PELE, recently highlighted as an outstanding advance in an international blind competition and industrial benchmarks.We acknowledge the BSC-CRG-IRB Joint Research Program in Computational Biology. This work was supported by a grant
from the Spanish Government CTQ2016-79138-R.J.I. acknowledges support from SVP-2014-068797, awarded by the Spanish Government.Peer ReviewedPostprint (author's final draft
- …