时光过客 发表于 2016-7-25 15:24:06

gromacs平衡体系问题

在做小分子蛋白复合物模拟时，调电荷之后mdrun,报错:
Step -1:
The charge group starting at atom 1342 moved than the distance allowed by the domain decomposition (3.417050) in direction Y
distance out of cell 2552.957462
Old coordinates:    3.610    2.696    2.358
New coordinates: 1610.154 2556.375    5.610
Old cell boundaries in direction Y:    0.000    3.417
New cell boundaries in direction Y:    0.000    3.417

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Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 4124

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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请问这怎么解决呀？？？

wangpengfei 发表于 2016-7-25 20:24:17

调电荷是指加过离子？

时光过客 发表于 2016-7-26 15:30:05

wangpengfei 发表于 2016-7-25 20:24
调电荷是指加过离子？

就是按照流程，体系中有非平衡电荷，需要加离子平衡体系
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