相关论文: A High-Throughput Steered Molecular Dynamics Study…
Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics…
Ion channels are important proteins for physiological information transfer and functional control. To predict the microscopic origins of their voltage-conductance characteristics, we here applied dissipation-corrected targeted Molecular…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics…
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure.…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Conventional molecular dynamics (MD) simulation approaches, such as $\textit{ab initio}$ MD (AIMD) and empirical force field MD (EFFMD), face significant trade-offs between physical accuracy and computational efficiency. This work presents…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…
Free energy calculations of two crystalline phases of the molecular compound S8 were performed via molecular dynamics simulations of these crystals. The elemental sulphur S8 molecule model used in our MD calculations consists of a…
The solid-liquid interface free energy \gamma sl is a key parameter controlling nucleation and growth during solidification and other phenomena. There are intrinsic difficulties in obtaining accurate experimental values, and the previous…
A molecular dynamics (MD) simulation is used to quantitatively analyze the induced membrane potential for an applied external field varied between 0.4 V/nm to 2.0 V/nm. The change in the electrostatic potential in the DPPC is directly…
Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy…
We analyze free energy estimators from simulation trials mimicking single-molecule pulling experiments on a neck linker of a kinesin motor. For that purpose, we have performed a version of steered molecular dynamics (SMD) calculations. The…
Ab initio molecular dynamics (AIMD) simulations employing density functional theory (DFT) and plane waves are routinely carried out using density functionals at the level of Generalized Gradient Approximation (GGA). AIMD simulations…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…