[gmx-users] the sum of the two largest charge group radii is larger than rlist

[morpheus]

Hi,

I get the following error:

"
Largest charge group radii for Van der Waals: 6.762, 6.758 nm
Largest charge group radii for Coulomb:       9.487, 9.465 nm

WARNING 1 [file md_vsIonDod.mdp]:
  The sum of the two largest charge group radii (18.951988) is larger than
  rlist (1.400000)
"

I found this on the gromacs webpage:

"A similar error ("The sum of the two largest charge group radii (X) is
larger than rlist") can arise under two circumstances:

   1. The charge groups are inappropriately large or rlist is set too low.
   2. Molecules are broken across periodic boundaries, which is not a
   problem in a periodic system.  In this case, the sum of the two largest
   charge groups will correspond to a value of twice the box vector along
   which the molecule is broken."


If I visualise my protein with VMD nothing seems to be broken across the
box boundary ... I also tried:

gmx trjconv -s JM22_onlyFullTCR_pbc.pr.pdb -f JM22_onlyFullTCR_pbc.pr.pdb
-o JM22_onlyFullTCR.pr.pdb -pbc whole

... but the warning stays the same - do I have a problem or can I just
ignore the warning?


Thanks!

M