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标题: charmm-gui生成的二面角参数在gmx2025.中的警告应该如何处理 [打印本页]

作者
Author: youknowdcf 时间: 2026-3-29 20:15
标题: charmm-gui生成的二面角参数在gmx2025.中的警告应该如何处理
本帖最后由 youknowdcf 于 2026-3-29 20:16 编辑

各位老师同学好，最近发现charmm-gui生成的二面角力场参数（类型为9）的会在gromacs 2025.X版本中提示警告，而在2024及以前的版本中则不会提示，查看了官方的更新说明：grompp now warns about identical dihedraltype 9 definitions. grompp would silently ignore double, identical dihedraltype definitions with function type 9. Now such entries are not ignored and a warning is generated.

开发者关于该问题讨论的地址是：https://gitlab.com/gromacs/gromacs/-/work_items/5333。
请问如何理解这个警告呢？是将其忽视还是应该在itp文件中将警告对应的参数行注释掉？

以下是警告内容：
WARNING 1 [file ffbonded.itp, line 23588]:
  Encountered a second line of parameters for dihedral type 9 for the same
  atom types with the same parameters. Will generate as many dihedral
  potentials for these atom types as there are parameter line entries. The
  line is:
  CG311 CG321 OG301 CG321    9  0.000000e+00  1.213360e+00    2

WARNING 2 [file ffbonded.itp, line 23590]:
  Encountered a second line of parameters for dihedral type 9 for the same
  atom types with the same parameters. Will generate as many dihedral
  potentials for these atom types as there are parameter line entries. The
  line is:
  CG311 CG321 OG301 CG321    9  0.000000e+00  1.799120e+00    3

WARNING 3 [file ffbonded.itp, line 23592]:
  Encountered a second line of parameters for dihedral type 9 for the same
  atom types with the same parameters. Will generate as many dihedral
  potentials for these atom types as there are parameter line entries. The
  line is:
  CG311 CG321 OG301 CG321    9  0.000000e+00  2.384880e+00    1

WARNING 4 [file ffbonded.itp, line 23620]:
  Encountered a second line of parameters for dihedral type 9 for the same
  atom types with the same parameters. Will generate as many dihedral
  potentials for these atom types as there are parameter line entries. The
  line is:
  CG321 CG311 OG301 CG321    9  0.000000e+00  1.673600e+00    1

WARNING 5 [file ffbonded.itp, line 23622]:
  Encountered a second line of parameters for dihedral type 9 for the same
  atom types with the same parameters. Will generate as many dihedral
  potentials for these atom types as there are parameter line entries. The
  line is:
  CG321 CG311 OG301 CG321    9  0.000000e+00  2.050160e+00    3

WARNING 6 [file ffbonded.itp, line 23630]:
  Encountered a second line of parameters for dihedral type 9 for the same
  atom types with the same parameters. Will generate as many dihedral
  potentials for these atom types as there are parameter line entries. The
  line is:
  CG321 CG321 OG301 CG311    9  0.000000e+00  1.213360e+00    2

WARNING 7 [file ffbonded.itp, line 23632]:
  Encountered a second line of parameters for dihedral type 9 for the same
  atom types with the same parameters. Will generate as many dihedral
  potentials for these atom types as there are parameter line entries. The
  line is:
  CG321 CG321 OG301 CG311    9  0.000000e+00  1.799120e+00    3

WARNING 8 [file ffbonded.itp, line 23634]:
  Encountered a second line of parameters for dihedral type 9 for the same
  atom types with the same parameters. Will generate as many dihedral
  potentials for these atom types as there are parameter line entries. The
  line is:
  CG321 CG321 OG301 CG311    9  0.000000e+00  2.384880e+00    1

作者
Author: Loading0760 时间: 2026-3-30 10:47
你先试试把同一个二面角的参数在ffbonded.itp里手动调整使之连续，看看会不会有警告。

多次定义同一个二面角，我以二面角CG311-CG321-OG301-CG321为例，它实际上是将多个余弦项相加，得到总的二面角能量贡献，公式如下：
V_dih = 2.384*(1+cos(1 * phi - 0.0)) + 1.213*(1+cos(2 phi -0.0 ) +1.799(1+cos(3 *phi -0.0 )
这个是2025版本的特性，以前遇到这种情况是忽略，现在当成警告了而已。详见更新公告https://manual.gromacs.org/docum ... ltype-9-definitions

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