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标题: gromacs新手请教一下关于生成tpr文件的问题 [打印本页]

作者
Author: 756300562 时间: 2021-5-11 11:46
标题: gromacs新手请教一下关于生成tpr文件的问题
请教各位老师，输入指令后提示这样的警告，不知道该怎么处理。

NOTE 1 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to -650907319
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 2 [file topol.top, line 48]:
  System has non-zero total charge: -31.000000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.

WARNING 1 [file topol.top, line 48]:
  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.

作者
Author: Lacrimosa 时间: 2021-5-11 11:49
如果体系的净电荷确实不为0 可以加上-maxwarn 10忽略warning

作者
Author: 牧生 时间: 2021-5-11 13:05
本帖最后由牧生于 2021-5-11 13:06 编辑

NOTE 1 可以不管，因为已经说明了，Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation.

NOTE 2 体系带电荷，不符合一般的电中性原则，需要加入抗衡离子。如果你确信此时的体系是带电的，可以忽略

WARNING 1 就是告诉你体系带电，如果忽略，就不会WARNING

忽略电荷的方法 -maxwarn 10

作者
Author: sobereva 时间: 2021-5-11 15:39
显然得用genion加抗衡离子

作者
Author: 756300562 时间: 2021-5-11 16:33
好的谢谢各位老师

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