[gmx-users] Grompp not producing tpr files
Peter Stern
peter.stern at weizmann.ac.il
Thu Jun 13 17:38:31 CEST 2019
A segmentation fault is a “crash” not a normal exit. The only information you have there is where the program got to before it crashed. No log file?
Peter
Sent from my iPhone
> On Jun 13, 2019, at 6:04 PM, 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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