[gmx-users] Segmentation fault (core dumped) version 4.6.*
Carlos Navarro Retamal
cnavarro at utalca.cl
Thu May 21 19:47:56 CEST 2015
Dear Chris,
Thanks a lot for your reply.
Indeed, my first files were create by using gromacs 5, so i created all of the files again, but now using 4.6.3 version.
Sadly the error is still appearing :/ (Even using gmxcheck)
:-) gmxcheck (-:
Option Filename Type Description
------------------------------------------------------------
-f traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-f2 traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-s1 top1.tpr Input, Opt. Run input file: tpr tpb tpa
-s2 top2.tpr Input, Opt. Run input file: tpr tpb tpa
-c topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb
-e ener.edr Input, Opt. Energy file
-e2 ener2.edr Input, Opt. Energy file
-n index.ndx Input, Opt. Index file
-m doc.tex Output, Opt. LaTeX file
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
-vdwfac real 0.8 Fraction of sum of VdW radii used as warning
cutoff
-bonlo real 0.4 Min. fract. of sum of VdW radii for bonded atoms
-bonhi real 0.7 Max. fract. of sum of VdW radii for bonded atoms
-[no]rmsd bool no Print RMSD for x, v and f
-tol real 0.001 Relative tolerance for comparing real values
defined as 2*(a-b)/(|a|+|b|)
-abstol real 0.001 Absolute tolerance, useful when sums are close to
zero.
-[no]ab bool no Compare the A and B topology from one file
-lastener string Last energy term to compare (if not given all are
tested). It makes sense to go up until the
Pressure.
Segmentation fault (core dumped)
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
On May 21, 2015 at 6:30:22 PM, Christopher Neale (chris.neale at alum.utoronto.ca<mailto:chris.neale at alum.utoronto.ca>) wrote:
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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