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

[cjalmeciga]

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

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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>>
> 
> -- 
> ==================================================
> 
> 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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