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付老师您好，我想向您请教一个关于meta-eABF参数——hillwidth的问题
您在帖子里说
“metadynamics {
colvars phi psi
这里同时向定义的两个几何变量的扩展自由度上施加metadynamics偏置力，即meta-eABF
hillwidth 5
metadynamics的峰宽（单位为width），在meta-eABF中均可使用5
hillweight 0.1
metadynamics的峰高（kcal/mol），在meta-eABF中均可使用0.1
}”
我对”metadynamics的峰宽（单位为width）“这句话不是很理解，然后就去查了些资料
namd user's guide里说：
“hillWidth < Width of a Gaussian hill, measured in number of grid points >
Context: metadynamics
Acceptable Values: positive decimal
Description: The value of this keyword is the Gaussian width 2σξi, expressed in number of
grid points: the grid spacing is determined by width (see 9.3.8). The values of the parameter
σξi for each variable ξi inits physical units are printed by NAMD at initialization time. Values
between 1 and 3 are recommended: smaller values fail to adequately interpolate each Gaussian
[30], while larger values may be unable to account for steep free-energy gradients.”
namd官网上又说:
"hillWidth <Relative width of a Gaussian hill with respect to the colvar's width>
Context: metadynamics
Default value: √(2Π) / 2
Acceptable values: positive decimal
Description: The Gaussian width along each colvar, 2σ, is set as the product between this number and the colvar's parameter wi given by width (see 13.2.1); such product is printed in the standard output of VMD. The default value of this number gives a Gaussian hill function whose volume is equal to the product of Π×wi, the volume of one histogram bin (see 13.5.7), and W.
我的理解是如果cv的width = 5（单位°），hillwidth = 5，则添加的每个能量的hillwidth的值为5×5=25（单位°），请问这样理解对吗
我在做meta-eABF的时候，cv选的是distance z，但不慎把hillwidth设成0.5了，请问这个对结果影响大吗，是否可以通过延长模拟时间来弥补这个失误呀...
感谢老师指导 |
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发表于 Post on 2019-11-29 12:44:12
楼主 Author
