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

2013-11-11 Thread 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
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Baltimore, MD 21201

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

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

2013-11-11 Thread Carlos Javier Almeciga Diaz 
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?



Carlos Javier Alméciga Díaz, QF., PhD.

Profesor Asistente

Pontificia Universidad Javeriana

Facultad de Ciencias

Instituto de Errores Innatos del Metabolismo

Tel: 57-1-3208320 Ext 4140-4099

Fax: 57-1-3208320 Ext 4099

Bogotá. D.C. - COLOMBIA

cjalmec...@javeriana.edu.co

http://www.javeriana.edu.co/ieim

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