[gmx-users] Re: segmentation fault on gromacs 4.5.5 after mdrun

[Justin Lemkul]

On 11/12/13 12:14 PM, cjalmeciga wrote:
>
> The output of energy minimization was
>
> Potential Energy  = -1.42173622068236e+06
> Maximum force     =  9.00312066109319e+02 on atom 148
> Norm of force     =  2.06087515037187e+01
>

OK, reasonable enough.  How about a description of what the system is, which 
force field you chose, how you derived the ligand topology, and the full 
contents of your .mdp file?

-Justin

> Thanks
>
> Javier
>
>
> Justin Lemkul wrote
>> On 11/12/13 10:58 AM, cjalmeciga wrote:
>>> I run
>>>
>>> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
>>>
>>> and everything looks fine. I check the nvt.tpr, and temperature is ok.
>>>
>>
>> The fact that grompp completes indicates there is nothing syntactically
>> wrong
>> with the input files.  Whether or not the content of the .mdp is
>> physically
>> sensible or the input configuration is plausible is an entirely different
>> matter.  Please tell us what the exact outcome of the previous energy
>> minimization was (potential energy, maximum force, copied and pasted from
>> screen
>> output or .log file).
>>
>>> the real problem is with the mdrun function.
>>>
>>> could be a problem of the software?
>>>
>>
>> You have presented no evidence that would lead anyone to believe the
>> problem is
>> with mdrun.  In the vast majority of cases, user input is the problem.
>>
>> -Justin
>>
>>> Thanks
>>>
>>> Javier
>>>
>>>
>>>
>>> Justin Lemkul wrote
>>>> On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote:
>>>>> Hello evryone,
>>>>>
>>>>> I doing a simulation of a ligand-protein interaction with gromacs
>>>>> 4.5.5.
>>>>> Everything looks fine after I equilibrate the protein-ligand complex.
>>>>> I'm
>>>>> running these commands:
>>>>>
>>>>>
>>>>> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
>>>>>
>>>>> mdrun -deffnm nvt
>>>>>
>>>>> Nevertheless, I got this error:
>>>>>
>>>>> "Reading file nvt.tpr, VERSION 4.5.5 (double precision)
>>>>> Segmentation fault"
>>>>>
>>>>> What should I do?
>>>>>
>>>>
>>>> Instantaneous failure typically indicates that the forces are
>>>> nonsensically high
>>>> and the constraint algorithm immediately fails.  Likely the previous
>>>> energy
>>>> minimization did not adequately complete.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 601
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>
>>>> jalemkul at .umaryland
>>>
>>>>    | (410) 706-7441
>>>>
>>>> ==================================================
>>>> --
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>>> View this message in context:
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>>>
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>
>> jalemkul at .umaryland
>
>>   | (410) 706-7441
>>
>> ==================================================
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> --
> View this message in context: http://gromacs.5086.x6.nabble.com/segmentation-fault-on-gromacs-4-5-5-after-mdrun-tp5012431p5012464.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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