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

[cjalmeciga]

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 real problem is with the mdrun function.

could be a problem of the software?

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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