[gmx-users] Error message while running energy minimization

Wed Jul 13 19:19:28 CEST 2016

I modified the em.mdp file

; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep      = 0.01      ; Energy step size
nsteps = 500000   ; Maximum number of (minimization) steps to perform
energygrps = Protein UNK ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1    ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.4 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.4 ; long range electrostatic cut-off
rvdw = 1.4 ; long range Van der Waals cut-off
pbc    = xyz ; Periodic Boundary Conditions (yes/no)
epsilon-rf     = 61

When I try putting rcoulomb =0.8 as you had suggested, I get this error
message
ERROR 1 [file em.mdp]: With coulombtype = PME (without modifier), rcoulomb
must be equal to rlist, or rlistlong if nstcalclr=1. For optimal energy
conservation,consider using a potential modifier.
Do I need to use a potential modifier as it suggests?

On Wed, Jul 13, 2016 at 12:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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