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标题: gromacs模拟EC和DMC的混合溶液生成tpr文件电荷不为零求助 [打印本页]

作者
Author: adong 时间: 2020-7-13 22:43
标题: gromacs模拟EC和DMC的混合溶液生成tpr文件电荷不为零求助
EC 和 DMC 小分子的力场文件我用 LigParGen 网站生成的，提取出 [atomtypes] 放在atomtypes.itp中，EC 和 DMC 的成键参数放在各自的 itp 中，并在top文件中include。准备能量最小化生成tpr文件是提示：总的电荷量不为零，不知道哪里有问题？求助如何解决报错信息：
Command line:
  gmx_mpi grompp -f em.mdp -c blank.gro -p top.top -o em.tpr

Setting the LD random seed to -981595758
Generated 343206 of the 343206 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 343206 of the 343206 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'EC'
Excluding 3 bonded neighbours molecule type 'DMC'

NOTE 1 [file top.top, line 20]:
  System has non-zero total charge: -0.024994
  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 top.top, line 20]:
  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.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net
Charge
J. Chem. Theory Comput. 10 (2014) pp. 381-393
-------- -------- --- Thank You --- -------- --------

Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 500    Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 18747.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 42x42x42, spacing 0.119 0.119 0.119
Estimate for the relative computational load of the PME mesh part: 0.24
This run will generate roughly 1 Mb of data

There was 1 note

There was 1 warning

-------------------------------------------------------
Program:    gmx grompp, version 2018.4
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2406)

Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.

作者
Author: sobereva 时间: 2020-7-14 07:31
用Multiwfn算CM5电荷，乘上1.2，作为1.2*CM5电荷放到里面去，这比ligpargen自动产生的电荷结果更好，这点在http://sobereva.com/266一开始说了。而且Multiwfn输出电荷小数位数多，可以避免加和偏离0明显的问题。当前DMC的原子电荷加和轻微偏离0，显然DMC分子数目多的时候偏离0就会更显著。

作者
Author: adong 时间: 2020-7-14 09:12
好的，谢谢sob老师，我试一下Multiwfn算CM5

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