[gmx-users] Fwd: Residue 1 mapping problem?

[Justin Lemkul]

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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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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