[gmx-users] core dump

[Dallas Warren]

http://www.gromacs.org/Documentation/Errors#Pressure_scaling_more_than_1.25

System is unstable, there is a problem with with your topology or
coordinates.

On Fri, 6 Mar. 2020, 6:53 am Mohamed Abdelaal, <m.b.abdelaal at gmail.com>
wrote:

> Hello everybody
>
> I have been using GROMACS 2018.1 in the last month and I got an error "core
> dumped" while running the simulation. Accordingly, I have installed the
> 2020.1 version and while I am doing pressure equilibration (npt), I had the
> same error again (I paste it below) which is core dumped. Is it a problem
> in this version or I might have done something wrong while running the
> equilibration ?
>
> I would really appreciate it, if anyone can guide me. I have pasted the
> error below
>
> Thanks
> Mohamed
>
>                   :-) GROMACS - gmx mdrun, 2020.1 (-:
>
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> GROMACS:      gmx mdrun, version 2020.1
> Executable:   /home/abdelaal/build2/gromacs-2020.1/build/bin/gmx
> Data prefix:  /home/abdelaal/build2/gromacs-2020.1 (source tree)
> Working dir:  /home/abdelaal/Desktop/GROMACS/C60:TAPC/C60_GRM/22
> Command line:
>   gmx mdrun -v -deffnm npt
>
> Reading file npt.tpr, VERSION 2020.1 (single precision)
> Changing nstlist from 10 to 100, rlist from 1 to 1
>
> Using 1 MPI thread
>
> Non-default thread affinity set, disabling internal thread affinity
>
> Using 8 OpenMP threads
>
> starting mdrun 'GRM in vacuum'
> 50000 steps,     25.0 ps.
> step 44700, remaining wall clock time:   137 s
> Step 44790  Warning: pressure scaling more than 1%, mu: 1.01937 1.01937
> 1.01937
> Segmentation fault (core dumped)
> --
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