[gmx-users] Grompp not producing tpr files
Paul Bauer
paul.bauer.q at gmail.com
Thu Jun 13 17:09:11 CEST 2019
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, <israele at 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-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Bratin
> Kumar Das <177cy500.bratin at nitk.edu.in>
> Sent: Wednesday, June 12, 2019 7:00:55 PM
> To: gmx-users at 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.abraham at 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, <israele at 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
> > > --
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