Hi, I fixed that error.
However,I now encounter a new one... GROMACS: gmx grompp, VERSION 5.0.2 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf 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) 2001-2014, 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 5.0.2 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx grompp -f mdp/min.mdp -o min -pp min -po min Setting the LD random seed to 1842076191 Generated 349030 of the 349030 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 349030 of the 349030 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'LIG' Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Number of degrees of freedom in T-Coupling group rest is 11837.00 Estimate for the relative computational load of the PME mesh part: 0.17 gcq#309: "Nobody Never Learnt No-Nothing from No History" (Gogol Bordello) GROMACS: gmx mdrun, VERSION 5.0.2 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf 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) 2001-2014, 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 5.0.2 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm min Reading file min.tpr, VERSION 5.0.2 (single precision) Using 1 MPI thread Using 8 OpenMP threads mpirun noticed that job rank 0 with PID 18038 on node compute-0-20.local exited on signal 11 (Segmentation fault). What is segmentation fault? What am I supposed to do? Please tell me. Thanks, Vidya.R On Mon, Sep 11, 2017 at 7:27 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Yeah I've never seen that, so I assume it's something weird related to how > GROMACS was originally compiled vs how the system has been updated since. > Since a rebuild is the way to investigate that, definitely update to at > least the latest 5.0.x while you do it. > > Mark > > On Mon, Sep 11, 2017 at 3:36 PM Wes Barnett <w.barn...@columbia.edu> > wrote: > > > On Mon, Sep 11, 2017 at 8:44 AM, Vidya R <vidyadevi2...@gmail.com> > wrote: > > > > > Hi, > > > > > > > > > When I give these two commands > > > > > > gmx grompp -f mdp/min.mdp -o min -pp min -po min > > > gmx mdrun -deffnm min > > > > > > I get this error. > > > > > > What to do? > > > > > > > > > > > > Reading file min.tpr, VERSION 5.0.2 (single precision) > > > tMPI error: tMPI Initialization error (in valid comm) > > > > > > Thanks, > > > Vidya.R > > > > > > > I can't speak to that exact error, but there have been several bug fix > > releases to the 5.0.x series since 5.0.2, so an upgrade may be in order. > I > > would even suggest upgrading to the latest release (2016.x series). > > > > > > -- > > James "Wes" Barnett > > Postdoctoral Research Scientist > > Department of Chemical Engineering > > Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> > > Columbia University > > w.barn...@columbia.edu > > http://wbarnett.us > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? 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