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 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

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

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