On 8/22/17 5:28 AM, morpheus wrote:
Thanks!
Is this also just a note or is there a problem?
"
WARNING 1 [file md_vsIonDod.mdp]:
The sum of the two largest charge group radii (18.373196) 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 ...
This seems to come up from grompp frequently and I can't figure out why
(if nothing is truly broken across PBC). It's totally irrelevant if
you're using the Verlet cutoff scheme, since charge groups are ignored.
-Justin
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