[gmx-users] Error in lipid_protein simulation ( Energy minimization)

Justin Lemkul jalemkul at vt.edu
Mon Jul 13 13:44:22 CEST 2015

On 7/13/15 12:42 AM, shabana yasmeen wrote:
> Dear Users!
>   I am doing simulation of protein and lipids but facing problem in
> energy minimization as I run:
> grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
>   i received Warnings as:
> WARNING 1 [file ffnonbonded.itp, line 3098]:
>    Overriding LJ-14 parameters.

Be careful here, because your force field is either redundant (harmless) or 
broken (bad news).

> WARNING 2 [file minim.mdp]:
>    The sum of the two largest charge group radii (8.718670) is larger than
>    rlist (1.300000)
> I don't understand how to resolve these warnings.. If I ignore them
> then at next step (mdrun -v -deffnm em) I get fatal error as:
> Fatal error:
> There is no domain decomposition for 12 nodes that is compatible with
> the given box and a minimum cell size of 8.61095 nm
> Change the number of nodes or mdrun option -rdd

This suggests either have a broken structure of some sort but it's impossible to 
tell based solely on this information.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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