[gmx-users] Error message while running energy minimization
Justin Lemkul
jalemkul at vt.edu
Wed Jul 13 19:52:12 CEST 2016
On 7/13/16 1:48 PM, Deep Bhattacharya wrote:
> Thanks. So I was looking at my ligand topology for the largest charged
> group, it is the SDmso type of atom. This was generated using PRODRG
> How can I fix this if this is the issue?
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OA 1 UNK OHF 1 -0.723 15.9994
> 2 SDmso 1 UNK SHD 1 2.191 32.0600
> 3 OM 1 UNK OHE 1 -1.188 15.9994
> 45 OA 1 UNK OGF 8 -0.189 15.9994
> 46 SDmso 1 UNK SGG 8 2.191 32.0600
> 47 OA 1 UNK OGI 8 -0.722 15.9994
>
> Please help
>
Each of those charge groups has three atoms (unless you've chopped out the rest
of each), so no, that is not the problem grompp is complaining about. Again,
with the Verlet cutoff scheme, the message is completely irrelevant.
In general, don't use PRODRG topologies that have not been carefully refined.
They are of poor quality and this is likely a contributor to your instability.
-Justin
> On Wed, Jul 13, 2016 at 12:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/13/16 1:19 PM, Deep Bhattacharya wrote:
>>
>>> 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?
>>>
>>>
>> You need to set rlist = rcoulomb = rvdw as has already been stated. Note
>> that rcoulomb becomes somewhat flexible when using PME, so you don't
>> necessarily *need* to stick to 0.8.
>>
>> -Justin
>>
>>
>> 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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>>>>
>>>
>>>
>>>
>> --
>> ==================================================
>>
>> 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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>> Gromacs Users mailing list
>>
>> * Please search the archive at
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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
==================================================
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