[gmx-users] Error message while running energy minimization

[Justin Lemkul]

On 7/13/16 12:25 PM, Deep Bhattacharya wrote:
> Hello,
>
> This is the error message that I am getting trying to run energy
> minimization
>

It's not an error, it's a note.  That means, "for your information, here is 
something you may want to check."  It does not necessarily mean anything is 
wrong (that's what an "error" is).

> NOTE 2 [file topol.top]:
>   The largest charge group contains 11 atoms.
>   Since atoms only see each other when the centers of geometry of the charge
>   groups they belong to are within the cut-off distance, too large charge
>   groups can lead to serious cut-off artifacts.
>   For efficiency and accuracy, charge group should consist of a few atoms.
>   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>

So look at your topology.  Where's your largest charge group?  If you're using 
the Verlet cutoff scheme, it's completely irrelevant. You don't specify a 
cutoff-scheme explicitly your .mdp but it is the default in recent versions, but 
you haven't said which GROMACS version you're using.

-Justin

> em.mdp
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> define       =  -DPOSRES -DPOSRES_LIGAND
> integrator = steep
> emtol = 1000.0
> emstep      = 0.01
> nsteps = 500000
> energygrps              = System
> nstlist    = 1
> rlist               = 1.4
> ns_type    = grid
> coulombtype    = PME
> rcoulomb    = 1.4
> vdwtype        = cut-off
> rvdw    = 1.4
> pbc    = xyz
> epsilon-rf     = 61
>
> Please help
>
> *Deep S Bhattacharya*
>
> *Graduate Research Assistant*
>
> Mohs Biomedical Imaging & Nanotechnology Group
>
> Pharmaceutical Sciences
>
> *University of Nebraska Medical Center*
>
> 4018 Eppley Science Hall  |  Omaha, NE 68198-6805
>
> office 402.559.4349  | cell 402.906.1640
>
> deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com
>

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================