[gmx-users] the sum of the two largest charge group radii is larger than rlist
morpheus.sommer2008 at gmail.com
Wed Jul 5 15:18:09 CEST 2017
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
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?
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