一篇用NAMD模拟发表的文章，可以帮你理解模拟的精神

Electro-osmotic screening of the DNA charge in a nanopore
Binquan Luan and Aleksei Aksimentiev
Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, USA
Received 29 October 2007; published 26 August 2008

Extensive all-atom molecular dynamics simulations were performed to characterize the microscopic origin of the force experienced by DNA in a bulk electrolyte and a solid-state nanopore when subject to an external electrostatic field E. The effective screening of the DNA charge was found to originate from the hydrodynamic drag of the electro-osmotic flow that is driven by the motion of counterions along the surface of DNA. We show that the effective driving force F in a nanopore obeys the same law as in a bulk electrolyte: F= E,
where   and   are the friction coefficient and electrophoretic mobility of DNA, respectively. Using this relationship, we suggest a method for determining the effective driving force on DNA in a nanopore that does not require a direct force measurement.

不知道为什么无法上传附件，把DOI贴下面
DOI: 10.1103/PhysRevE.78.021912  PACS number s : 87.14.G , 87.15.Tt, 87.15.A

[ 本帖最后由 redream 于 2008-9-2 18:59 编辑 ]

那么调参数这件事情对应于实验中的什么事情呢？

做试验上做不到的事情啊，实验室无法达到的参数空间，计算机可以做，呵呵

很大程度上，计算是计算，实验是实验。

哈。。。在现在的模拟技术下，非常同意xxx的观点。。。

事实上，不管我们现在承认不承认，做实验的人从心底里是不相信模拟的。如果做的结果跟他们一样，他们会很乐意采纳模拟的意见和结果，如果不一样。。。。nobody cares us。。。

唉。。。我个人是被做实验的羞辱惯了。。。

但是模拟技术毕竟还在发展，无论是计算机硬件，还是算法以及应用软件都在发展。所以基本上本人持乐观态度，虽然当前现实依然残酷。。。。

[ 本帖最后由 xubest 于 2008-9-7 14:05 编辑 ]

我目前对计算还是实验都是浅尝而已，说说我的看法，或者说是幻想

实验中，基本的现象貌似都没有什么意思，捕捉一些新的现象，奇特的现象，大都能建立新的理论，现实一些说，发一些很好的paper

计算呢，不知道为什么，我不太敢相信计算中得到的很新奇的现象，既然计算模拟建立在统计理论的基础上，那我就觉得那些异常仅仅是异常，不知道我说的对不对
对于模拟的看法，我偏向于认为它是思维实验，在脑袋里构思一个实验过程，预料一个结果，然后用计算机去实现它

计算较之实验的优势，除了成本上，我觉得最好就就是计算能做实验不能做的事情（尺度上，等等），基于此，我认为，计算得到的很常规的现象和数据（并不一定是多么奇特），也是很有参考价值的

做计算机模拟的，应该都是现实世界的预言家，嘿嘿

One key reason that ones concern about simulations is the parameters! In principle, the parameters are designed for some situations based on the experiments, and it is not clear whether it is right or not do for the new DISCOVERY. Quite a lot researchers do not check the reliability !

If there is no stone, simulation can only fly in the sky!

目前的试验和模拟应该是相辅相成的。模拟也算一种技术，将来会被更先进技术取代的，或者说会变的不流行的。问题是模拟会生存多久？

'模拟也算一种技术,'
I can not fully agree. Simuatlion is totally based on Physics and Chemistry at different level.  Computer is just a way to solve the equation. You can say ' computer may be replaced by some other technology'.

现在的公认理论也许将来就被推翻了

呵呵，实际上我一直认为没有绝对真理

Scientist always  believes in nothing but himself.
Suddenly I notice that this, NAMD, is chenjung085's field.
,sorry

[ 本帖最后由 water 于 2008-9-12 04:29 编辑 ]

不同观点很正常 要么大家都是机器人啦。
我对NAMD是初学者，这里也不是我的底盘哦，大家都自由发表自己的看法呢

Great Leader!

Theory has his field!