During the energy minimization step, I faced the error, Segmentation fault (core dumped).
ruhul@ruhul:~/Documents/glucosidase_acarbose$ gmx grompp -f em.mdp -c complex_solv_ions.gro -p topol.top -o em.tpr
:-) GROMACS - gmx grompp, 2021.4-Ubuntu-2021.4-2 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/ruhul/Documents/glucosidase_acarbose
Command line:
gmx grompp -f em.mdp -c complex_solv_ions.gro -p topol.top -o em.tpr
Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’
NOTE 1 [file em.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 2108389175
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117432 of the 167910 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘UNK1’
Excluding 2 bonded neighbours molecule type ‘SOL’
Excluding 3 bonded neighbours molecule type ‘NA’
Analysing residue names:
There are: 844 Protein residues
There are: 1 Other residues
There are: 34648 Water residues
There are: 28 Ion residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group rest is 247413.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 100x100x100, spacing 0.119 0.119 0.119
Estimate for the relative computational load of the PME mesh part: 0.14
This run will generate roughly 9 Mb of data
There was 1 note
GROMACS reminds you: “Big Data is like teenage sex: everyone talks about it, nobody really knows how to do it, everyone thinks everyone else is doing it, so everyone claims they are doing it…” (Dan Ariely)
ruhul@ruhul:~/Documents/glucosidase_acarbose$ gmx mdrun -v -deffnm em
:-) GROMACS - gmx mdrun, 2021.4-Ubuntu-2021.4-2 (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, version 2021.4-Ubuntu-2021.4-2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/ruhul/Documents/glucosidase_acarbose
Command line:
gmx mdrun -v -deffnm em
hwloc/linux: Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don’t enable unless really needed).
Compiled SIMD: SSE4.1, but for this host/run AVX_512 might be better (see
log).
Reading file em.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
WARNING: Listed nonbonded interaction between particles 1708 and 1723
at distance 3.088 which is larger than the table limit 2.200 nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
WARNING: Listed nonbonded interaction between particles 10657 and 10668
at distance 2.240 which is larger than the table limit 2.200 nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.12842e+06 Fmax= 8.55878e+05, atom= 1721
Step= 1, Dmax= 1.0e-02 nm, Epot= 1.05464e+06 Fmax= 8.45427e+05, atom= 1721
Step= 2, Dmax= 1.2e-02 nm, Epot= 9.82093e+05 Fmax= 8.33549e+05, atom= 1721
Step= 3, Dmax= 1.4e-02 nm, Epot= 9.08068e+05 Fmax= 8.20059e+05, atom= 1721
Step= 4, Dmax= 1.7e-02 nm, Epot= 8.30460e+05 Fmax= 8.04537e+05, atom= 1721
Step= 5, Dmax= 2.1e-02 nm, Epot= 7.47492e+05 Fmax= 7.86157e+05, atom= 1721
Step= 6, Dmax= 2.5e-02 nm, Epot= 6.57615e+05 Fmax= 7.63404e+05, atom= 1721
Step= 7, Dmax= 3.0e-02 nm, Epot= 5.59553e+05 Fmax= 7.33839e+05, atom= 1721
Step= 8, Dmax= 3.6e-02 nm, Epot= 4.52647e+05 Fmax= 6.94270e+05, atom= 1721
Step= 9, Dmax= 4.3e-02 nm, Epot= 3.38191e+05 Fmax= 6.41107e+05, atom= 1721
Step= 10, Dmax= 5.2e-02 nm, Epot= 2.21109e+05 Fmax= 5.74613e+05, atom= 1723
Step= 11, Dmax= 6.2e-02 nm, Epot= 1.27301e+05 Fmax= 4.13466e+06, atom= 1721
Step= 12, Dmax= 7.4e-02 nm, Epot= 1.05686e+05 Fmax= 5.12493e+05, atom= 1721
Step= 13, Dmax= 8.9e-02 nm, Epot= -4.82345e+04 Fmax= 1.12132e+06, atom= 1721
Step= 15, Dmax= 5.3e-02 nm, Epot= -8.49790e+04 Fmax= 7.07140e+05, atom= 1721
Step= 16, Dmax= 6.4e-02 nm, Epot= -1.35405e+05 Fmax= 5.68419e+05, atom= 1721
Step= 17, Dmax= 7.7e-02 nm, Epot= -2.06407e+05 Fmax= 5.05072e+05, atom= 1721
Step= 18, Dmax= 9.2e-02 nm, Epot= -2.85788e+05 Fmax= 4.82860e+05, atom= 1721
Step= 19, Dmax= 1.1e-01 nm, Epot= -3.75818e+05 Fmax= 1.25992e+06, atom= 10668
Step= 20, Dmax= 1.3e-01 nm, Epot= -3.89227e+05 Fmax= 3.14067e+05, atom= 10668
Step= 21, Dmax= 1.6e-01 nm, Epot= -4.49212e+05 Fmax= 8.62527e+06, atom= 1723
Step= 22, Dmax= 1.9e-01 nm, Epot= -5.00556e+05 Fmax= 3.38298e+06, atom= 1368
Step= 23, Dmax= 2.3e-01 nm, Epot= -5.38831e+05 Fmax= 2.53930e+05, atom= 1723
Step= 24, Dmax= 2.8e-01 nm, Epot= -7.45281e+05 Fmax= 9.59912e+05, atom= 10668
Segmentation fault (core dumped)
Sir, May I know how to solve this?