[gmx-users] Broken molecule across periodic boundary: "The sum of the two largest charge group radii (xxx) is larger than rlist (xxx)"

[yunshi11 .]

Hi there,

I understand this is an old issue, but no one seems to have a solution?

So I want to take a snapshot from the middle of a MD trajectory (like 67ns
point from a 100ns trajectory), preferably with all solvent molecules
(waters and ions). However, after using trjconv -pbc to make molecules
"whole" or "nojump", I am still having the same warning:

......
Number of degrees of freedom in T-Coupling group Water_and_ions is 314583.28
Largest charge group radii for Van der Waals: 11.794, 9.979 nm
Largest charge group radii for Coulomb:       11.794, 11.748 nm

WARNING 1 [file nvt.mdp]:
  The sum of the two largest charge group radii (23.542278) is larger than
  rlist (1.000000)


Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 112x112x112, spacing 0.120 0.120 0.120
Estimate for the relative computational load of the PME mesh part: 0.27
This run will generate roughly 42 Mb of data

There was 1 warning

-------------------------------------------------------
Program grompp, VERSION 4.6.5
Source code file:
/global/software/src/gromacs/gromacs-4.6.5/src/kernel/grompp.c, line: 1910

Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I have also tried removing solvents (partially and completely), and found
that I could only resolve this issue after removing all of the solvents
(waters and ions).

Regards,
Yun