发信人: Ag (小坡), 信区: Biology
标 题: Re: 请教几个molecular dynamics软件
发信站: Unknown Space - 未名空间 (Fri Nov 14 14:31:53 2003), 站内信件


The charge difference is becuase they use different fitting method.
After each force field is generated, they testify it with proteins/DNAs
which studied a lots experimentally.

At the beginning, I didn't trust MD also. The same reason with you,
quantum effect can't be simualted with classical method. But later,
I changed my idea. I found MD has enough theoritical support.

Yes. MD has lots of shortcoming now. But it has good future.


【 在 Rizhard (快乐的狗) 的大作中提到: 】
: if you look at page 17, you can notice how diffferent the charges on
: different Force Field, the most significant difference is even close
: to 100%, so whose simulation are you going to believe??? You know,
: all of these are used to produce papers.
: Newton's theory is ok for rocket but not for light, the same,
: MD is ok for things much bigger than protein, or things have much simple
: energy surface such as hydrogen gas, but for proteins which have a lot of
: quantum effect on the biological function, it is impossible to simulate
: that using the over simplified force field. A simple example, many proteins
: have more than one conformation, can you get the other conformation if
: we knows one by using MD? For decades, nobody can do that.
: 【 在 Ag (小坡) 的大作中提到: 】
: : I think the two authors must say something interesting can be provided
: : by MD simulation. Did you notice that?
: : According to einstein, Newton is wrong. so what? Newton still can help
: : you send rocket into space.


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