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@.umaryland > | (410) 706-7441 > > ================================================== > -- > gmx-users mailing list > gmx-users@ > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to > gmx-users-request@ > . > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/segmentation-fault-on-gromacs-4-5-5-after-mdrun-tp5012431p5012458.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
