Parallel MD–Simulation of Synthetic Polymer Chains

نویسندگان

  • Bernd Jung
  • Hans-Peter Lenhof
  • Peter Müller
  • Christine Rüb
چکیده

We have developed and implemented parallel algorithms for the molecular dynamics simulation of synthetic polymer chains. Our package has been specifically designed for distributed–memory machines like the widespread Cray T3E, but it can also be used on clusters of workstations and on a single workstation (i.e., it runs also sequentially). The target molecules are single synthetic polymer chains in solution.

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

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Simulating Synthetic Polymer Chains in Parallel

We have investigated algorithms that are particularly suited for the parallel MD simulations of synthetic polymers. These algorithms distribute the atoms of the polymer among the processors. Dynamic non{ bonded interactions, which are the diicult part of an MD simulation, are realised with the help of a special coarse{grained representation of the chain structure. We have devised and compared a...

متن کامل

Parallel Computing of Polymer Chains Based on Monte Carlo Method

Computer simulation of polymer chain is carried out by Monte Carlo method in this paper. The properties of polymer chain are simulated by self avoiding walk and bond fluctuation model. The parallel computing model is established to solve the physical problems of the polymer chains. We analyze the algorithms for polymer chains to parallel computing at high performance computing center. Gustafson...

متن کامل

Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking

In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 (HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first hep...

متن کامل

Dissipative Particle Dynamics simulation hydrated Nafion EW 1200 as fuel cell membrane in nanoscopic scale

The microphase separation of hydrated perfluorinated sulfonic acid membrane Nafion was investigated using Dissipative Particle Dynamics (DPD). The nafion as a polymer was modelled by connecting coarse grained beads which corresponds to the hydrophobic backbone of polytetrafluoroethylene and perfluorinated side chains terminated by hydrophilic end particles of sulfonic acid groups [1, 2]. Each f...

متن کامل

On the Pseudo Phase Diagram of Single Semi-Flexible Polymer Chains: A Flat-Histogram Monte Carlo Study

Abstract: Local stiffness of polymer chains is instrumental in all structure formation processes of polymers, from crystallization of synthetic polymers to protein folding and DNA compactification. We present Stochastic Approximation Monte Carlo simulations—a type of flat-histogram Monte Carlo method—determining the density of states of a model class of single semi-flexible polymer chains, and,...

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

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

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 1999