The output of energy minimization was Potential Energy = -1.42173622068236e+06 Maximum force = 9.00312066109319e+02 on atom 148 Norm of force = 2.06087515037187e+01
Thanks Javier Justin Lemkul wrote > On 11/12/13 10:58 AM, cjalmeciga wrote: >> 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 fact that grompp completes indicates there is nothing syntactically > wrong > with the input files. Whether or not the content of the .mdp is > physically > sensible or the input configuration is plausible is an entirely different > matter. Please tell us what the exact outcome of the previous energy > minimization was (potential energy, maximum force, copied and pasted from > screen > output or .log file). > >> the real problem is with the mdrun function. >> >> could be a problem of the software? >> > > You have presented no evidence that would lead anyone to believe the > problem is > with mdrun. In the vast majority of cases, user input is the problem. > > -Justin > >> 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. >> > > -- > ================================================== > > 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-tp5012431p5012464.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