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标题: 求助：forcite 模拟有机物在金属表面吸附时总是出错 [打印本页]

作者
Author: 小刚仔 时间: 2023-1-9 08:14
标题: 求助：forcite 模拟有机物在金属表面吸附时总是出错

---- Dynamics parameters ----

Ensemble                      : NVT
Temperature                   : 298.00 K
  Control method             : Nose
  Q ratio                      : 0.0100000
Timestep                      : 1.00 fs
Number of steps                : 500
Duration                      : 0.5 ps
Initial velocities             : Random
Random number seed             : 1673190047

---- Energy parameters ----

Forcefield                   : Universal
Charges                      : Use current
Electrostatic terms:
  Summation method             : Ewald
  Accuracy                   : 0.01 kcal/mol
  Buffer width                : 0.5 A

van der Waals terms:
  Summation method             : Atom based
  Truncation method          : Cubic spline
  Cutoff distance             : 9.5 A
  Spline width                : 1 A
  Long range correction       : YES
  Buffer width                : 0.5 A

---- Thermostat ----

Nose mass parameter, Q mass: 6.00477 kcal/mol*ps^2

---- Constraints ----

Position constraints          : 90

Dynamics calculation - Aborting dynamics.
An unphysical integration step (>100 Angstroms) has been detected.
Try relaxing the structure with geometry optimization, reducing the time step,
reducing the temperature or a combination of these.

作者
Author: 牧生 时间: 2023-1-9 09:39
先试试换力场再说
Universal是针对金属离子的，不能用于单质金属。

作者
Author: 小刚仔 时间: 2023-1-9 11:16

牧生发表于 2023-1-9 09:39
先试试换力场再说
Universal是针对金属离子的，不能用于单质金属。

谢谢你，换了力场了，还是不行
---- Dynamics parameters ----

Ensemble                      : NVT
Temperature                   : 298.00 K
  Control method             : Nose
  Q ratio                      : 0.0100000
Timestep                      : 1.00 fs
Number of steps                : 500
Duration                      : 0.5 ps
Initial velocities             : Random
Random number seed             : 1673234054

---- Energy parameters ----

Forcefield                   : COMPASS (Version 2.8)
Charges                      : Forcefield assigned
Electrostatic terms:
  Summation method             : Ewald
  Accuracy                   : 0.01 kcal/mol
  Buffer width                : 0.5 A

van der Waals terms:
  Summation method             : Atom based
  Truncation method          : Cubic spline
  Cutoff distance             : 9.5 A
  Spline width                : 1 A
  Long range correction       : YES
  Buffer width                : 0.5 A

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Unable to calculate the ForcefieldType for particle 'RU1'
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The typing engine has been unable to assign a forcefield type.
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The typing engine has been unable to assign a forcefield type.
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The typing engine has been unable to assign a forcefield type.
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The typing engine has been unable to assign a forcefield type.
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Could not calculate the forces.
The typing engine has failed to calculate a forcefield type for 90 particles.
Try using a different forcefield or assign types manually (and remember to turn off the automatic calculation of forcefield types).

作者
Author: 小刚仔 时间: 2023-1-9 11:24
直接使用compass力场对金属结构优化都不行

---- Geometry optimization parameters ----

Algorithm                      : Smart
Convergence tolerance:
  Energy                      : 0.001 kcal/mol
  Force                      : 0.5 kcal/mol/A
Maximum number of iterations : 500
Motion groups rigid          : NO

---- Energy parameters ----

Forcefield                   : COMPASS (Version 2.8)
Charges                      : Forcefield assigned
Electrostatic terms:
  Summation method             : Ewald
  Accuracy                   : 0.001 kcal/mol
  Buffer width                : 0.5 A

van der Waals terms:
  Summation method             : Atom based
  Truncation method          : Cubic spline
  Cutoff distance             : 12.5 A
  Spline width                : 1 A
  Buffer width                : 0.5 A

Unable to calculate the ForcefieldType for particle 'RU1'
The typing engine has been unable to assign a forcefield type.
No typing rules found that match (except the wildcard '?').

Unable to calculate the ForcefieldType for particle 'RU1'
The typing engine has been unable to assign a forcefield type.
No typing rules found that match (except the wildcard '?').

Unable to calculate the ForcefieldType for particle 'RU1'
The typing engine has been unable to assign a forcefield type.
No typing rules found that match (except the wildcard '?').

Unable to calculate the ForcefieldType for particle 'RU1'
The typing engine has been unable to assign a forcefield type.
No typing rules found that match (except the wildcard '?').

Unable to calculate the ForcefieldType for particle 'RU1'
The typing engine has been unable to assign a forcefield type.
No typing rules found that match (except the wildcard '?').

Unable to calculate the ForcefieldType for particle 'RU1'
The typing engine has been unable to assign a forcefield type.
No typing rules found that match (except the wildcard '?').

Unable to calculate the ForcefieldType for particle 'RU1'
The typing engine has been unable to assign a forcefield type.
No typing rules found that match (except the wildcard '?').

Unable to calculate the ForcefieldType for particle 'RU1'
The typing engine has been unable to assign a forcefield type.
No typing rules found that match (except the wildcard '?').

Unable to calculate the ForcefieldType for particle 'RU1'
The typing engine has been unable to assign a forcefield type.
No typing rules found that match (except the wildcard '?').

Unable to calculate the ForcefieldType for particle 'RU1'
The typing engine has been unable to assign a forcefield type.
No typing rules found that match (except the wildcard '?').

The typing engine has failed to calculate a forcefield type for 10 particles.
Try using a different forcefield or assign types manually (and remember to turn off the automatic calculation of forcefield types).
Unable to calculate energy and gradients.
Geometry optimization finished with an error condition.

作者
Author: 卡开发发 时间: 2023-1-9 11:25

小刚仔发表于 2023-1-9 11:16
谢谢你，换了力场了，还是不行
---- Dynamics parameters ----

你选择的力场可能恰好不包含你体系当中原子对之间作用的类型。有机物得看何种有机物，有些有机物可以在金属表面产生特性吸附，甚至在MD过程中会发生成键断键，一般的力场不见得能正确描述，你可能需要调研下其他计算方案。

作者
Author: 小刚仔 时间: 2023-1-9 11:27

卡开发发发表于 2023-1-9 11:25
你选择的力场可能恰好不包含你体系当中原子对之间作用的类型。有机物得看何种有机物，有些有机物可以在金 ...

这样，文献里用的是compass力场的，不过我的有机物不一样，新的物质，还没文献报道的，那怎么办呢

作者
Author: 卡开发发 时间: 2023-1-9 11:45

小刚仔发表于 2023-1-9 11:27
这样，文献里用的是compass力场的，不过我的有机物不一样，新的物质，还没文献报道的，那怎么办呢

看牵不牵扯到成键断键的事情，比方说分子上有孤对电子直接配位到金属上的情况，我觉得一般力场基本上得不到太可靠的结果，这种情况会有点麻烦，可能要考虑专门的神经网络势或者半经验或者第一原理方法。其他方面可能我给不了特别专业的讨论和建议，你可以看看其他人的说法。

作者
Author: 小刚仔 时间: 2023-1-9 12:24

卡开发发发表于 2023-1-9 11:45
看牵不牵扯到成键断键的事情，比方说分子上有孤对电子直接配位到金属上的情况，我觉得一般力场基本上得不 ...

好的呢，谢谢你。我不懂这方面的

作者
Author: sobereva 时间: 2023-1-9 22:42
如果体系并不大，建议用CP2K等第一性原理程序在DFT级别做几何优化或动力学，比任何常见力场都靠谱得多。

作者
Author: 小刚仔 时间: 2023-1-9 23:59

sobereva 发表于 2023-1-9 22:42
如果体系并不大，建议用CP2K等第一性原理程序在DFT级别做几何优化或动力学，比任何常见力场都靠谱得多。

这......看不太懂，估计要花一段时间了呜呜呜

欢迎光临计算化学公社 (http://bbs.keinsci.com/)