求助：为什么gro和top文件原子数对不上

吧唧爱吃糖

求助各位找了半天没发现原子数对不上啊

casea

水的力场参数错了，tip4p是四点水模型，而你gro用的是三点水

牧生

看起来像是将单胞扩展以后，再加入了水和别的分子。你确认一下各个分子数量，以及gro里面是三点水模型还是四点水模型

吧唧爱吃糖

casea 发表于 2022-7-4 21:43
水的力场参数错了，tip4p是四点水模型，而你gro用的是三点水

谢谢解决了，确实是四点水模型没改

吧唧爱吃糖

牧生 发表于 2022-7-4 21:44
看起来像是将单胞扩展以后，再加入了水和别的分子。你确认一下各个分子数量，以及gro里面是三点水模型还是 ...

改了四点水模型，但是grompp的时候提示这个
The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing.

我没管他继续mdrun之后提示


Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

Steepest Descents converged to machine precision in 3152 steps,
but did not reach the requested Fmax < 1.
Potential Energy  = -8.80181406162373e+04
Maximum force     =  4.90022566027328e+02 on atom 1882
Norm of force     =  1.71190334880236e+01


请问一下师兄这个是怎么回事啊？以下是我的mdp文件和gro文件

吧唧爱吃糖

忽略上面的内个note修改emtol为500后发现min.gro变成了这样，不知道哪里有问题

吧唧爱吃糖

吧唧爱吃糖 发表于 2022-7-5 15:41
忽略上面的内个note修改emtol为500后发现min.gro变成了这样，不知道哪里有问题

解决了，打扰各位了