[gmx-users] Error message while running energy minimization

[Justin Lemkul]

On 7/13/16 1:05 PM, Deep Bhattacharya wrote:
> I am using GROMACS v.4.6. Does using Verlet cut-off scheme lead to problems
> like blowing up of the system?

No, you can't blame crashes on the Verlet algorithm.  It should be more accurate 
than anything else.  Systems typically crash because of (1) inadequate 
preparation/minimization, (2) bad topology, (3) inappropriate .mdp settings, or 
some combination thereof.

> When you say the largest charge in the topology you mean the combined
> protein-ligand pdb?

No, I mean the topology, not the coordinates.

> I have attached the .top and combined pdb file.
>

The list does not accept attachments, nor would any serve any purpose.  You can 
easily inspect the topology with a simple text editor.

-Justin

> 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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>
>
>

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

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

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