[gmx-users] Core dumped in NVT

[Mark Abraham]

Hi,

That something is the output of another program does not necessarily make
it a reasonable structure start MD. See
http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#lincs-settle-shake-warnings.
For example, some kind of void could exist that slams atoms around if you
haven't done a preliminary energy minimization, etc.

Mark

On Tue, May 1, 2018 at 2:06 PM Syed Azeem <syedazeemullah186 at gmail.com>
wrote:

> Hey all,
>
> I'm trying to simulate a peptide-protein docked complex. I docked the
> peptide using pepATTRACT package. After analysis, I selected the best
> pose and tried to simulate. This yielded an error and got core dumped
> in NVT equilibriation.
>
> I'm using GROMOS 54a7 force field. The error is pasted below:
>
> GROMACS:      gmx mdrun, VERSION 5.1.4
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>   gmx mdrun -v -deffnm nvt
>
>
> Running on 1 node with total 2 cores, 4 logical cores
> Hardware detected:
>   CPU info:
>     Vendor: GenuineIntel
>     Brand:  Intel(R) Core(TM) i3-4030U CPU @ 1.90GHz
>     SIMD instructions most likely to fit this hardware: AVX2_256
>     SIMD instructions selected at GROMACS compile time: AVX2_256
>
> Reading file nvt.tpr, VERSION 5.1.4 (single precision)
> Changing nstlist from 10 to 25, rlist from 1.4 to 1.434
>
> Using 1 MPI thread
> Using 4 OpenMP threads
>
>
> Step 0, time 0 (ps)  LINCS WARNING
>