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小木虫论坛-学术科研互动平台 » 计算模拟区 » 分子模拟 » DS/Sybyl/Autodock » 【求助】全原子模型和united atom模型的区别？
南方科技大学公共卫生及应急管理学院2025级博士研究生招生报考通知
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allenjobsf853

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[交流] 【求助】全原子模型和united atom模型的区别？

在论文上看见在进行模拟计算的时候，有些论文说采用全原子模型，而不采用united atom，请教一下，如何在模拟中体现出来使用的是哪种模型？

和同学讨论了一下，有人认为这个是根据使用的力场的不同来区分的，比如compass力场就是全原子模型，而有些力场就不是全原子模型


而我个人为是根据vdw和electrostatic的summation方法选择atom base和group base的不同造成的，如果将基团看做group base，应该就属于united atom了吧？

还是很迷惑，希望高人传道授业解惑下。  


先谢谢了

[ Last edited by zdhlover on 2009-12-10 at 15:32 ]
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1楼2008-12-18 12:40:03
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yyx19840628

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鹰的眼睛，狼的耳朵，豹的速 ...
俺一点也不懂啊，等你指教呢
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人生的最大遗憾莫过于错误地坚持了不该坚持的，轻易地放弃了不该放弃的……
2楼2008-12-18 14:42:57
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jqhejia

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yyx19840628(金币+1,VIP+0):xiexie
个人认为是根据使用的力场的不同来区分的，有的力场就是全原子模型，而有些力场如NERO就不是全原子模型。
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3楼2008-12-18 19:56:03
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allenjobsf853

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zzgyb(金币+2,VIP+0):谢谢你的参与，欢迎再次光临计算模拟版！
恩  我也是这么听人说的  但是也有同仁和我说如果你建立模型的时候如果讲某些基团，比如CH3作为一个整体进行计算的话，用一些全原子模型的力场，比如COMPASS力场也算是united-atom模型吧   

闹不清，比较困惑
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4楼2008-12-19 15:04:55
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wpllzx

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是啊，一直不被“全原子模型”和“联合原子模型”这两个概念迷惑？
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5楼2008-12-24 16:02:16
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wgpig

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lei0736(金币+4,VIP+0):谢谢 圣诞快乐
United Atom Force Fields and Reduced Representations
In our discussion so far, we have assumed that all of the atoms in the system are explicitly
represented in the model. However, as the number of non-bonded interactions scales with
the square of the number of interaction sites present, there are clear advantages if the
number of interaction sites can be reduced. The simplest way to do this is to subsume
some or all of the atoms (usually just the hydrogen atoms) into the atoms to which they
are bonded. A methyl group would then be modelled as a single 'pseudo-atom' or
'united atom'. The van der Waals and electrostatic parameters would be modified to take
account of the adjoining hydrogen atoms. Considerable computational savings are possible;
for example, if butane is modelled as a four-site model rather than one with twelve atoms
then the van der Waals interaction between two butane molecules involves the calculation
of sixteen terms rather than 144. Other hydrocarbons are often represented using united
atom models. Many of the earliest calculations on proteins used united atom representa-
representations In this case, not all of the hydrogen atoms in the protein are subsumed into their adja-
adjacent atoms, but just those that are bonded to carbon atoms. Hydrogen atoms bonded to polar
atoms such as nitrogen and oxygen are able to participate in hydrogen-bonding interactions,
which are modelled much better if these hydrogens are explicitly represented.
One drawback with a united atom force field is that chiral centres may be able to invert
during a calculation. This was found to be a problem with the united atom force fields for
proteins. The alpha carbon in the peptide unit (Ca in Figure 4.42) is bonded to a hydrogen
atom and to the side chain (glycine and proline are slightly different; see Section 10.1). A
united atom force field model would not explicitly include the alpha hydrogen. Unfortu-
Unfortunately, the stereochemistry at the alpha carbon can then invert during a calculation. This
should be avoided as the naturally occurring amino acids have a defined stereochemistry
(as shown in Figure 4.42). This inversion may be prevented through the use of an improper
torsion term (e.g. N-C—Ca-R) to keep the side chain in the correct relative position.
In a united atom force field the van der Waals centre of the united atom is usually associated
with the position of the heavy (i.e. non-hydrogen) atom. Thus, for a united CH3 or CH2
group the van der Waals centre would be located at the carbon atom. It would be more
accurate to associate the van der Waals centre with a position that was offset slightly
from the carbon position, in order to reflect the presence of the hydrogen atoms. Toxvaerd
has developed such a model that gives superior performance for alkanes than do the simple
united atom models, particularly for simulations at high pressures [Toxvaerd 1990]. In
Toxvaerd's model the interaction sites are located at the geometrical centres of the CH2 or
CH3 groups. The forces between these sites act on the united atom mass centre, which
remains located on the carbon atom (with a mass of 14 for a CH2 group and 15 for a CHj
group). As the interaction site is no longer located at an atomic nucleus the forces acting
on the masses are more complicated to calculate, but little additional computational expense
is required. The effect of using such an anisotropic potential is nicely illustrated by the two
arrangements of methylene units shown schematically in Figure 4.43. In the united atom
model both arrangements would have the same energies and forces, but this is not so
with the Toxvaerd anisotropic potential.
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6楼2008-12-25 09:00:16
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allenjobsf853

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7楼2008-12-26 12:34:40
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yzhhlq_1983

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lei0736(金币+4,VIP+0):谢谢 欢迎光临
all-atom 和 united-atom 模型不能说是根据立场来分的。例如著名的opls立场就有opls-aa(all-atom)和opls-ua(united-atom)两种形式。很明显all-atom体系的模拟计算
量要大于united-atom模型体系，而且相对要更准确。但并不是说united-atom是不合理的，因为CH3 group看成一个粒子（在united-atom模型中），仅仅是把C-H键和H-C-H角给近似掉了，主要因为这两种势能是属于硬自由度范围，对于模拟结果影响很小，往往是可以忽略的（所以模拟中键长常常固定往往是基于这个考虑）。
需要注明的，united-atom和文献中粗粒化模型不是一个概念，后者是通过对比结构参数（如RDF）等拟合得到参数，在大分子聚合物中常用
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8楼2009-01-06 13:23:40
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