𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Periodic boundary conditions and the correct molecular-dynamics ensemble

✍ Scribed by J.A. White; F.L. Román; A. González; S. Velasco

Publisher
Elsevier Science
Year
2008
Tongue
English
Weight
884 KB
Volume
387
Category
Article
ISSN
0378-4371

No coin nor oath required. For personal study only.

📜 SIMILAR VOLUMES

On the stability of boundary conditions
On the stability of boundary conditions for molecular dynamics
✍ Xiantao Li 📂 Article 📅 2009 🏛 Elsevier Science 🌐 English ⚖ 619 KB

We study the stability of boundary conditions for molecular dynamics simulations. A general stability criterion is established. We first consider a one-dimensional model with nearest neighbor interaction and multiple-neighbor interactions. We then generalize the results to more realistic models in 3

Molecular dynamics simulation in the gra
Molecular dynamics simulation in the grand canonical ensemble
✍ Hossein Eslami; Florian Müller-Plathe 📂 Article 📅 2007 🏛 John Wiley and Sons 🌐 English ⚖ 264 KB

## Abstract An extended system Hamiltonian is proposed to perform molecular dynamics (MD) simulation in the grand canonical ensemble. The Hamiltonian is similar to the one proposed by Lynch and Pettitt (Lynch and Pettitt, J Chem Phys 1997, 107, 8594), which consists of the kinetic and potential ene

A fast pairlist-construction algorithm f
A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions
✍ Tim N. Heinz; Philippe H. Hünenberger 📂 Article 📅 2004 🏛 John Wiley and Sons 🌐 English ⚖ 222 KB

## Abstract A new grid‐cell algorithm is presented that permits the fast construction of cutoff‐based nonbonded pairlists in molecular simulations under periodic boundary conditions based on an arbitrary box shape. The key features of the method are (1) the use of a one‐dimensional mask array (to d

The effect of box shape on the dynamic p
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions
✍ Tsjerk A. Wassenaar; Alan E. Mark 📂 Article 📅 2005 🏛 John Wiley and Sons 🌐 English ⚖ 362 KB 👁 1 views

## Abstract The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near‐densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that o