[gmx-users] grompp for minimization: note & warning

Justin Lemkul jalemkul at vt.edu
Mon Sep 16 13:47:05 CEST 2013

On 9/16/13 7:37 AM, shahab shariati wrote:
> Dear Justin
> About following warning in grompp using
> WARNING 1 [file em.mdp]:
> The sum of the two largest charge group radii (6.940482) is larger than
> rlist (1.200000)
> You said "You probably have molecules split across PBC in the input
> coordinate file. here's nothing wrong in that case"
> I mention that I used input coordinate file from folloowing web site"
> http://cmb.bio.uni-goettingen.de/cholmembranes.html. Structures in this
> website were equilibrated 195 ns.
> Nonetheless, has my input coordinate file problem?

I have no idea.  What file are you using?  Visual inspection will make it very 
obvious whether or not you have broken molecules.  My original guess was exactly 
that - a guess.  Based on the supposed size of the group in question, it seemed 
that it was probably a common membrane issue.  Maybe this is or is not the case.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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