【建议】不知道有没有人来增加分子动力学模拟部分

luckier

感觉现在ｓｉｍｗｅ越来越强了：）
各种模拟也都有各自的论坛了，不过不知道现在国内搞分子动力学的模拟
多不多？不管是MDS或是MC模拟，希望有能人来开一个，大家好有个地方交流交流！

simwe

希望能听到luckier 先生关于“分子动力学”更详细的介绍。合适的话，我们考虑增开这方面的版块。

wgao

simwe wrote:
希望能听到luckier 先生关于“分子动力学”更详细的介绍。合适的话，我们考虑增开这方面的版块。

是啊, 再介绍详细一些, 看看能不能开一个新版

bainhome

这样的会员直接ban掉！
在几个地方发同样这种垃圾！老大看看编程技术版、数学力学版、MATLAB版和建设家园版，根本就没有羞耻心，扣完分还在发！

[ 本帖最后由 bainhome 于 2006-11-27 21:22 编辑 ]

wgao

ID删除, IP禁止90天

tiny0o0

西工大的一个博士生，就搞这个的，今年刚去当洪堡学者了。。才走

oasis_luo

我也正奇怪为什么没有这个版块。有限元工程上应用比较广，但是科研上，
分子动力学在国外是数值计算的主流。当然，也可以把第一原理计算（密度
泛函理论）放在同一个版。强烈支持开一个关于nanoscale 或者 atomistic scale
数值模拟的版面。

molen

支持分子动力学。
最近我在研究Dissipative Particle Dynamics and its comparison with CFD.

不知道luckier先生有没有写好关于“分子动力学”更详细的介绍。如果暂时没有，我带是可以写一个简单介绍。

dava

支持！
这块几年前就想学学了，应该很有趣

xunbao

期待该板块的横空出世！搜索了一下，分子动力学分散在数学与力学科学版和编程语言版。

yuan

谁先来详细介绍一些有关此部分的知识。

staray

原帖由 oasis_luo 于 2006-12-12 12:18 发表
我也正奇怪为什么没有这个版块。有限元工程上应用比较广，但是科研上，
分子动力学在国外是数值计算的主流。当然，也可以把第一原理计算（密度
泛函理论）放在同一个版。强烈支持开一个关于nanoscale 或者 atom ...

分子动力学的数值计算也是应用得相当广泛的，特别是现在微纳尺度的研究更加需要这方面的研究。我也是刚开始接触这个，我知道可以用在微流体、计算材料等相当多的领域。

MD，MC，MDS，CPMD等，当然还有直接应用第一原理的，是比较常用的方法。
强烈支持增开相关的版面。

simulationstar

What is molecular dynamics?
  We call molecular dynamics (MD) a computer simulation technique where the time evolution of a set of interacting atoms is followed by integrating their equations of motion.
In molecular dynamics we follow the laws of classical mechanics, and most notably Newton's law:   (1)
for each atom i in a system constituted by N atoms. Here, mi is the atom mass, its acceleration, and  the force acting upon it, due to the interactions with other atoms. Therefore, in contrast with the Monte Carlo method, molecular dynamics is a deterministic technique: given an initial set of positions and velocities, the subsequent time evolution is in principle completely determined. In more pictorial terms, atoms will ``move'' into the computer, bumping into each other, wandering around (if the system is fluid), oscillating in waves in concert with their neighbors, perhaps evaporating away from the system if there is a free surface, and so on, in a way pretty similar to what atoms in a real substance would do.

The computer calculates a trajectory in a 6N-dimensional phase space (3N positions and 3N momenta). However, such trajectory is usually not particularly relevant by itself. Molecular dynamics is a statistical mechanics method. Like Monte Carlo, it is a way to obtain a set of configurations distributed according to some statistical distribution function, or statistical ensemble. An example is the microcanonical ensemble, corresponding to a probability density in phase space where the total energy is a constant E:



Here,  is the Hamiltonian, and  represents the set of positions and momenta.  is the Dirac function, selecting out only those states which have a specific energy E. Another example is the canonical ensemble, where the temperature T is constant and the probability density is the Boltzmann function


According to statistical physics, physical quantities are represented by averages over configurations distributed according to a certain statistical ensemble. A trajectory obtained by molecular dynamics provides such a set of configurations. Therefore, a measurements of a physical quantity by simulation is simply obtained as an arithmetic average of the various instantaneous values assumed by that quantity during the MD run.

Statistical physics is the link between the microscopic behavior and thermodynamics. In the limit of very long simulation times, one could expect the phase space to be fully sampled, and in that limit this averaging process would yield the thermodynamic properties. In practice, the runs are always of finite length, and one should exert caution to estimate when the sampling may be good (``system at equilibrium'') or not. In this way, MD simulations can be used to measure thermodynamic properties and therefore evaluate, say, the phase diagram of a specific material.

Beyond this ``traditional'' use, MD is nowadays also used for other purposes, such as studies of non-equilibrium processes, and as an efficient tool for optimization of structures overcoming local energy minima (simulated annealing).

homeboy

http://simulation.5d6d.com/index.php
刚建的

allenxiaoyan

分子动力学是一个不错的方向，建议增加。