[gmx-users] Error message while running energy minimization

[Deep Bhattacharya]

I am using GROMACS v.4.6. Does using Verlet cut-off scheme lead to problems
like blowing up of the system?
When you say the largest charge in the topology you mean the combined
protein-ligand pdb?
I have attached the .top and combined pdb file.

Please help
Deep

On Wed, Jul 13, 2016 at 11:56 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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-- 
Deep Bhattacharya.
Post-Graduate Student,
Department of Pharmaceutical Chemistry,
Bombay College Of Pharmacy.
Mobile - +918976129616