nvt打包时warning求助

lucies123

Command line:
  gmx grompp -f nvt.mdp -c em1.gro -p topol.top -o nvt1.tpr -r em1.gro -n index.ndx         

NOTE 1 [file nvt.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy

WARNING 1 [file topol.top, line 65]:
  There are atoms at both ends of an angle, connected by constraints and
  with masses that differ by more than a factor of 13. This means that
  there are likely dynamic modes that are only very weakly coupled. To
  ensure good equipartitioning, you need to either not use constraints on
  all bonds (but, if possible, only on bonds involving hydrogens) or use
  integrator = sd or decrease one or more tolerances:
  verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=
  4 or SHAKE tolerance <= 1e-05


NOTE 2 [file nvt.mdp]:
  This run will generate roughly 14072 Mb of data

There were 2 notes
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.


打包nvt文件时产生的warning1，请教下是否可以忽略？查看top文件的65行，是加的抗衡离子NAnvt.mdp中constraints一项，是用的constraints=all-bonds，是否和这个有关？要如何修正呢？

sobereva

没有特殊必要绝对不要用all-bonds，完全是自取其辱。论坛里我说过N次

lucies123

sobereva 发表于 2022-1-20 22:46
没有特殊必要绝对不要用all-bonds，完全是自取其辱。论坛里我说过N次

好的，谢谢sob老师，我再去学习下