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

Justin Lemkul jalemkul at vt.edu
Thu Aug 24 03:22:13 CEST 2017

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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