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

[Justin Lemkul]

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

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