Gromacs问题 Q&A

Posted by XiLock on February 10, 2019

Google找不到可以在这个mail box里找一下,里面有很多相关的提问和回答:mail-archive


… no domain decomposition for 20 ranks…
Fatal error:
There is no domain decomposition for 20 ranks that is compatible with the given box and a minimum cell size of 0.929375 nm  
Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings  
Look in the log file for details on the domain decomposition  
For more information and tips for troubleshooting, please check the GROMACS website at  

Solution: Use following command line: gmx mdrun -v -deffnm em -nt 8
I used the option “-nt 1” to make it work. Sometimes the simulation is too small to be divided.
sob老师说是因为原子数较少所致的域分解错误,可以用-ntmpi 1解决。

参见Gromacs Errors

2019.2 build warnings

开发者说:The warning are harmless, something happened in the build infrastructure which emits some new warnings that we’ve not caught before the release.
具体参见:[gmx-users] 2019.2 build warnings


A:amber99力场描述高浓度离子不合理,当年sob老师也遇到了相同的问题(doi: 10.3866/PKU.WHXB201506191),后来改用KBFF力场就没问题了。明显是amber力场的缺陷。

  1. Joung I S, Cheatham III T E. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations[J]. The journal of physical chemistry B, 2008, 112(30): 9020-9041.
  2. Auffinger P, Cheatham T E, Vaiana A C. Spontaneous formation of KCl aggregates in biomolecular simulations: a force field issue?[J]. Journal of chemical theory and computation, 2007, 3(5): 1851-1859. (文中的rmin应为0.5rmin)
  3. Joung I S, Cheatham III T E. Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters[J]. The Journal of Physical Chemistry B, 2009, 113(40): 13279-13290. (文献1基础上考察更多参数)
Right hand side ‘1.0 1.0’ for parameter ‘tau_p’ in parameter file is not a real value

参见mailing list: strange behaviout in 5.1.2



Step 500, time 0.5 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 178.962402, max 279.656189 (between atoms 2 and 3)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      3      4   85.1    4.1929  58.3083      0.2700
      3      5   89.2    2.6759  61.9056      0.2700
      4      5  157.9    2.7246  41.7282      0.2700
  1. 这种错误往往是因为topol不合理而导致的,比如约束过多的话为了满足一些约束而超出另一些约束的阈值。
  2. 别都用键长约束,可以换用键角的时候用键角约束替换掉一些键长约束。(如嘉兴之前做Fmoc的时候中间五元环简化成3个珠子,如果用三个键长来约束的话就会爆炸,如果用两个键长加一个键角的话就正常了。)
  3. 注意二面角的0°和180°是不一样的,跟表面序号有关系。(from Supernova)


Note 2 [file, line 45]:
  The bond in molecule-type MoS between atoms 1 S1 and 6 Mo1 has an
  estimated oscillational period of 6.9e-03 ps, which is less than 10 times
  the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.