标题: 能量最小化后NVT 升温初始步 LINCS 崩溃（madrid 2019的H3O+体系，CUDA error #700） [打印本页] 作者Author: kogareru1z 时间: yesterday 03:29 标题: 能量最小化后NVT 升温初始步 LINCS 崩溃（madrid 2019的H3O+体系，CUDA error #700） 我在对纯H3O+体系进行nvt升温测试时模拟崩溃。我首先进行了能量最小化，log显示如下：
NOTE 1 [file init.top, line 14]:
System has non-zero total charge: 8.500000
Total charge should normally be an integer. See https://manual.gromacs.org/current/user-guide/floating-point.html
for discussion on how close it should be to an integer.
WARNING 1 [file init.top, line 14]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a physiological salt concentration.
NOTE 2 [file em.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing.
但最后还是成功收敛了： (, 下载次数 Times of downloads: 1)
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但之后进行nvt升温模拟，程序报错崩溃 (, 下载次数 Times of downloads: 2)
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我认为是[constraints]导致的问题，当我注释掉H-H的约束条件后，模拟可以进行，但HOH的角度无法控制，H3O+不是刚体而且结构明显不合理 (, 下载次数 Times of downloads: 3)