Segementation error while running em

User discussions
1

GROMACS version:2019
GROMACS modification: No
Here post your question : I run the cammand “gmx mdrun -v -deffnm em”
and getting this output:

                  :-) GROMACS - gmx mdrun, 2019.6 (-:

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GROMACS: gmx mdrun, version 2019.6
Executable: /share/apps/packages/gromacs/installation/bin/gmx
Data prefix: /share/apps/packages/gromacs/installation
Working dir: /export/
Command line:
gmx mdrun -deffnm em -v

Back Off! I just backed up em.log to ./#em.log.2#
Reading file em.tpr, VERSION 2019.6 (single precision)
Using 1 MPI process
Using 24 OpenMP threads

1 GPU selected for this run.
Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
PP:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU

Back Off! I just backed up em.trr to ./#em.trr.2#

Back Off! I just backed up em.edr to ./#em.edr.2#

Steepest Descents:
Tolerance (Fmax) = 1.00000e+05
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.55967e+35 Fmax= inf, atom= 42
Segmentation fault

i have check my server my job run for few seconds and then end. Kindly guide.

2

Dear Rija,
this is due to high forces appearing in your em (see line “Step= 0, Dmax= 1.0e-02 nm, Epot= 1.55967e+35 Fmax= inf, atom= 42” → Fmax=inf)

Something seems to be bad about your initial configuration and atom 42 seems to overlap with another one. Sometimes it helps not to use GPUs and few CPU cores, as (for me) using MPI and/or GPU seems to be more unstable.

Best Fabian

3

Dear Fabian,

Thanks for your help. Is there a way that I can change the coordinates of my overlapping atoms. Which file should I looked into or run again?
As I am using gromacs on official system so CPU core option is not possible.

Grateful,
Rijja

4

Dear Rijja,
yes, you can modify your input structure file (.pdb, .gro, …), though this is a tedious task. I recommend checking the protocol for creating your input structure file.
Before you start important simulations I also highly recommend going through all or at least some of the GROMACS Tutorials to get used to the different file types and its contents of gromacs.
Best
Fabian