Hello, Yes, the last part indicates an error that should not happen.
Which version did you use to run this? If it is a version before 2018, can you try the newer versions to see if the error persists? Cheers Paul On Thu, 13 Jun 2019, 17:04 Israel Estrada, <isra...@cpp.edu> wrote: > Thanks for the replies! > > Mark, the process seemed to "finish" properly (my terminal did not close, > and the command line was waiting for the next command as if it ran > normally). I looked for the output file (ions.tpr) in the working > directory, or any new files, but nothing was generated. > > Bratin, here is what my terminal displayed, > "command line: > gmx grompp -f ions.mdp -c box.gro -o ions.tpr -p topol.top > > Setting the LD random seed to 973096069 > Segmentation fault (core dumped)" > The last part seems to be the error, right? > > Thanks again!! > -Israel > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Bratin > Kumar Das <177cy500.bra...@nitk.edu.in> > Sent: Wednesday, June 12, 2019 7:00:55 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Grompp not producing tpr files > > Hi > Give here the full error > > On Thu 13 Jun, 2019, 1:35 AM Mark Abraham, <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > Was grompp exiting normally, or crashing? Are you looking in the right > > place, for a file of the right name? :-) > > > > Mark > > > > On Wed., 12 Jun. 2019, 18:42 Israel Estrada, <isra...@cpp.edu> wrote: > > > > > Hello users, > > > > > > > > > I'm running into problems trying to grompp; I'm using the command > > > > > > > > > gmx grompp -f ions.mdp -c etc_box.gro -o ions.tpr -p topol.top > > > > > > > > > and the process shows no error messages, but output files are not being > > > generated. I'm running this on a small molecule, about 20 atoms, with > the > > > hopes that I can modify OPLS parameters as needed. I'm sure the problem > > is > > > related to an error in the topology files, but I don't know how or if I > > can > > > fix this. > > > > > > > > > Any help would be greatly appreciated, thank you! > > > > > > -Israel > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > > https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Cisraele%40cpp.edu%7Cffac6cb3efc64f49b25008d6efa30958%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636959880859561003&sdata=srifcVMGyR34i8jY1w3JwmR%2F25Azq3Bf%2Ft39u5u82wc%3D&reserved=0 > before > > > posting! > > > > > > * Can't post? 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