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Re: 请教几个molecular dynamics软件
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Re: 请教几个molecular dynamics软件# Biology - 生物学
Ag
1
我想即使是namd的头也不敢象你这么大口气说话,呵呵。
amber的force fields,模拟DNA是最强的,无可比拟。
charmm的package比较大,分析处理数据,还有一些辅助分析手段比较完善一些。
gromos gromacs不太清楚,后者好像是前者的衍生。
NAMD好像比较新,没有了解。
我觉得没有所谓的活力前途比较一说,主要还是network的问题。
karplus派系出来的人,多用charmm。kollman派系出来的,多用amber。
欧洲那边的,多用gromos。
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e*e
2
all the force fields you listed are supported in namd.

【在 Ag 的大作中提到】
: 我想即使是namd的头也不敢象你这么大口气说话,呵呵。
: amber的force fields,模拟DNA是最强的,无可比拟。
: charmm的package比较大,分析处理数据,还有一些辅助分析手段比较完善一些。
: gromos gromacs不太清楚,后者好像是前者的衍生。
: NAMD好像比较新,没有了解。
: 我觉得没有所谓的活力前途比较一说,主要还是network的问题。
: karplus派系出来的人,多用charmm。kollman派系出来的,多用amber。
: 欧洲那边的,多用gromos。

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e*e
3
there are tons of reasons other than parameters could lead to
problems, such as the time scale, energy function, etc. you
would always have experiments for comparison. It is
impossible to make every parameter perfect. The important
thing is that you may discover something new with MD, and
the new discovery can be further examined with experiments.
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Ag
4
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.
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