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标题: 求助:gmx区域分解cell size大于盒子尺寸 [打印本页]

作者
Author:
wzx    时间: 2021-5-8 10:55
标题: 求助:gmx区域分解cell size大于盒子尺寸
盒子8.4*8.4*28.4 nm3,其中z方向有3/4真空层。区域分解显示最小单元格尺寸大于盒子尺寸,好像是成键作用最大距离太大导致的。成键作用最大距离为啥会这么大,该如何改进?

Initializing Domain Decomposition on 16 ranks
Dynamic load balancing: locked
Using update groups, nr 19590, average size 2.6 atoms, max. radius 0.139 nm
Minimum cell size due to atom displacement: 0.658 nm
Initial maximum distances in bonded interactions:
    two-body bonded interactions: 11.770 nm, Exclusion, atoms 6833 6837
  multi-body bonded interactions: 11.770 nm, Angle, atoms 6833 6837
Minimum cell size due to bonded interactions: 12.947 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Using 8 separate PME ranks
Optimizing the DD grid for 8 cells with a minimum initial size of 16.184 nm
Ewald_geometry=3dc: assuming inhomogeneous particle distribution in z, will not decompose in z.
The maximum allowed number of cells is: X 0 Y 0 Z 1


体系是模拟蛋白在GO层上的吸附,我冻结了GO层。


作者
Author:
sobereva    时间: 2021-5-8 11:43
贴图方式不对,别人看不到
作者
Author:
wzx    时间: 2021-5-8 14:12
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请老师们赐教




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