[gmx-users] Segmentation fault (core dumped) version 4.6.*

[Christopher Neale]

Dear Carlos:

Are you using a .top file from gromacs 5 with your gromacs 4 runs? If so, try regenerating your topology (and .itp files) using gromacs 4 (with GMXLIB set correctly). Not sure if that would even cause a problem, but it seems like it probably would and is the only thing that comes to mind.

If that is not the issue, then do any of the other commands work without a segfault (e.g. gmxcheck)?

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Carlos Navarro Retamal <cnavarro at utalca.cl>
Sent: 21 May 2015 11:55
To: gmx-users at gromacs.org
Subject: [gmx-users] Segmentation fault (core dumped) version 4.6.*

Dear gmx users,
In order to run my simulations, i usually used the 5.0.* version of gromacs without problems, but since i want to performed umbrella sampling simulations (and since the option pull_geometry=position is not available for the latest versions)
For that,  i installed the 4.6.7 version of gromacs.
The installation went without issue, but every time i used a command from gromacs i got the Segmentation fault (core dumped) error:
Like for example, by using this command line:
grompp -f npt_production.mdp -c npt_equilibration.gro -p topol.top -o npt_production.tpr
i got this:
Option     Filename  Type         Description
------------------------------------------------------------
  -f npt_production.mdp  Input        grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c npt_equilibration.gro  Input        Structure file: gro g96 pdb tpr etc.
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n      index.ndx  Input, Opt.  Index file
  -p      topol.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o npt_production.tpr  Output       Run input file: tpr tpb tpa
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file
-ref     rotref.trr  In/Out, Opt. Full precision trajectory: trr trj cpt

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel
-[no]v       bool   no      Be loud and noisy
-time        real   -1      Take frame at or first after this time.
-[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
                            sites
-maxwarn     int    0       Number of allowed warnings during input
                            processing. Not for normal use and may generate
                            unstable systems
-[no]zero    bool   no      Set parameters for bonded interactions without
                            defaults to zero instead of generating an error
-[no]renum   bool   yes     Renumber atomtypes and minimize number of
                            atomtypes

Segmentation fault (core dumped)
That is not telling me anything useful :/
I tried also installing the 4.6.3, but sadly i have the same problems with this version.
Hope someone can help me.
Best,
Carlos
--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl

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