GROMACS modification: No
Hi Gromacs users,
I am having an error when I run the MDsimulation. My system is made up of about 8000H2O and some NaCl. The box length of my system is (x y z)6.258999825nm 6.258999825nm 30.129999161nm
grompp shows a warning that
WARNING 1 [file 5.20.mdp]:
The sum of the two largest charge group radii (4.720785) is larger than
According to the Gromacs Manual(Common errors when using GROMACS — GROMACS 2022.2 documentation), the reasons might be
- The charge groups are inappropriately large
- rlist is set too low.
- Molecules are broken across periodic boundaries
- [mdp] settings are incompatible with the chosen algorithms
I did not declare the composition of the charge group. I don’t input the index.ndx file by myself and I think rlist is high enough.
I checked the g96 input file, no molecule is broken across the boundary in the beginning. Some molecules near the boundary look like
310 H2O OICE1 1237 5.442989349 6.236528873 15.018712997
310 H2O HICE2 1238 5.531808376 6.224104881 15.052166939
310 H2O HICE3 1239 5.404839039 6.303023815 15.076030731
310 H2O MW4 1240 5.449808598 6.243805885 15.030929565
The strange thing is, the charge group is extremely high and exceeds half of my box.
I am not sure where the problem is. Does anyone have any suggestions?
btw, if I use the maxwarn option to ignore the warning of grompp, the following mdrun will have a fatal error.
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
I try to make the step smaller, but it didn’t work, Does anyone have any suggestions?
my mdp file