[gmx-users] Segmentation fault
Xavier Periole
X.Periole at rug.nl
Sat Dec 22 14:42:05 CET 2007
A lincs warning at the step number 2 suggests that there is
something really wrong in your starting structure. Check it
in detail and a energy minimization should help.
XAvier
On Fri, 21 Dec 2007 23:36:30 -0800 (PST)
jahanshah ashkani <ashkani_2003 at yahoo.com> wrote:
> Sorry for the delay. What happened before the segmentation fault was:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -s WTpreMD.tpr Input Generic run input: tpr tpb tpa xml
> -o traj.trr Output Full precision trajectory: trr trj
> -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)
> -c WTpreMDres.gro Output Generic structure: gro g96 pdb xml
> -e ener.edr Output Generic energy: edr ene
> -g md.log Output Log file
> -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
> -field field.xvg Output, Opt. xvgr/xmgr file
> -table table.xvg Input, Opt. xvgr/xmgr file
> -tablep tablep.xvg Input, Opt. xvgr/xmgr file
> -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96
>pdb
> -tpi tpi.xvg Output, Opt. xvgr/xmgr file
> -ei sam.edi Input, Opt. ED sampling input
> -eo sam.edo Output, Opt. ED sampling output
> -j wham.gct Input, Opt. General coupling stuff
> -jo bam.gct Output, Opt. General coupling stuff
> -ffout gct.xvg Output, Opt. xvgr/xmgr file
> -devout deviatie.xvg Output, Opt. xvgr/xmgr file
> -runav runaver.xvg Output, Opt. xvgr/xmgr file
> -pi pull.ppa Input, Opt. Pull parameters
> -po pullout.ppa Output, Opt. Pull parameters
> -pd pull.pdo Output, Opt. Pull data output
> -pn pull.ndx Input, Opt. Index file
> -mtx nm.mtx Output, Opt. Hessian matrix
> -dn dipole.ndx Output, Opt. Index file
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -nice int 19 Set the nicelevel
> -deffnm string Set the default filename for all file options
> -[no]xvgr bool yes Add specific codes (legends etc.) in the output
> xvg files for the xmgrace program
> -np int 1 Number of nodes, must be the same as used for
> grompp
> -nt int 1 Number of threads to start on each node
> -[no]v bool no Be loud and noisy
> -[no]compact bool yes Write a compact log file
> -[no]sepdvdl bool no Write separate V and dVdl terms for each
> interaction type and node to the log file(s)
> -[no]multi bool no Do multiple simulations in parallel (only with
> -np > 1)
> -replex int 0 Attempt replica exchange every # steps
> -reseed int -1 Seed for replica exchange, -1 is generate a seed
> -[no]glas bool no Do glass simulation with special long range
> corrections
> -[no]ionize bool no Do a simulation including the effect of an X-Ray
> bombardment on your system
>
>
> Back Off! I just backed up md.log to ./#md.log.5#
> Reading file WTpreMD.tpr, VERSION 3.3.2 (single precision)
>
> Back Off! I just backed up ener.edr to ./#ener.edr.5#
>
> Step -2, time -0.004 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 1.349301 (between atoms 1113 and 1115) rms 0.035397
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 1104 1106 58.3 0.1456 0.2551 0.1470
> 1106 1107 58.9 0.1530 0.2667 0.1530
> 1106 1111 64.3 0.1533 0.1159 0.1530
> 1111 1112 80.4 0.1231 0.1854 0.1230
> 1111 1113 41.2 0.4557 0.1995 0.1330
> 1113 1114 82.4 0.0996 0.0968 0.1000
> 1113 1115 80.8 0.1476 0.3453 0.1470
> 1115 1116 62.3 0.1531 0.2768 0.1530
> 1115 1119 77.7 0.1517 0.2741 0.1530
> 1116 1117 36.3 0.1423 0.1747 0.1430
> 1121 1122 80.7 0.0992 0.1188 0.1000
> 1121 1123 84.8 0.1477 0.2245 0.1470
> 1123 1124 44.6 0.1517 0.2118 0.1530
> 1123 1137 43.4 0.1521 0.2093 0.1530
>
> Step -1, time -0.002 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.933924 (between atoms 1111 and 1113) rms 0.024333
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 1106 1111 92.2 0.1159 0.1138 0.1530
> 1111 1112 53.2 0.1854 0.0685 0.1230
> 1111 1113 59.6 0.1995 0.2572 0.1330
> 1113 1114 91.9 0.0968 0.1353 0.1000
> 1113 1115 62.5 0.3453 0.2040 0.1470
> 1115 1116 38.8 0.2768 0.1783 0.1530
> 1115 1119 61.2 0.2741 0.2458 0.1530
> 1119 1120 78.7 0.1051 0.1090 0.1230
> 1121 1122 44.4 0.1188 0.1374 0.1000
> 1121 1123 52.0 0.2245 0.2043 0.1470
> 1123 1137 35.9 0.2093 0.1656 0.1530
> starting mdrun '? in water'
> 250000 steps, 500.0 ps.
>
>
> Back Off! I just backed up traj.trr to ./#traj.trr.5#
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 16002.615234 (between atoms 1113 and 1114) rms 421.562012
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 161 162 63.3 0.1090 0.1092 0.1090
> 1087 1089 43.8 0.1470 0.2111 0.1470
> 1089 1090 41.6 0.1530 0.2121 0.1530
> 1089 1093 65.1 0.1530 0.6815 0.1530
> 1093 1094 57.4 0.1230 0.6487 0.1230
> 1093 1095 70.3 0.1332 7.4581 0.1330
> 1095 1096 63.4 0.1002 6.9145 0.1000
> 1095 1097 87.2 0.1477 38.1974 0.1470
> 1097 1098 87.4 0.1537 38.3103 0.1530
> 1097 1102 46.0 0.1563 93.5811 0.1530
> 1098 1099 74.2 0.1431 8.7328 0.1430
> 1098 1101 71.4 0.1531 8.6649 0.1530
> 1099 1100 73.2 0.1000 0.5716 0.1000
> 1102 1103 81.3 0.1266 123.2126 0.1230
> 1102 1104 101.3 0.1498 345.5438 0.1330
> 1104 1105 100.3 0.1138 339.2171 0.1000
> 1104 1106 73.4 0.2551 1196.1974 0.1470
> 1106 1107 73.8 0.2667 1298.7706 0.1530
> 1106 1111 115.0 0.1159 1137.4712 0.1530
> 1107 1108 156.6 0.1678 272.5244 0.1530
> 1108 1109 49.9 0.1545 96.5447 0.1530
> 1108 1110 81.5 0.1545 73.5228 0.1530
> 1111 1112 131.6 0.1854 528.7211 0.1230
> 1111 1113 80.4 0.1995 1840.3479 0.1330
> 1113 1114 93.7 0.0968 1600.3616 0.1000
> 1113 1115 89.2 0.3453 1596.2660 0.1470
> 1115 1116 89.7 0.2768 128.4722 0.1530
> 1115 1119 94.4 0.2741 131.9932 0.1530
> 1116 1117 90.0 0.1747 50.8581 0.1430
> 1117 1118 72.9 0.1024 0.8743 0.1000
> 1121 1122 176.1 0.1188 9.3235 0.1000
> 1121 1123 149.0 0.2245 5.8261 0.1470
> 1123 1124 120.6 0.2118 1.7661 0.1530
> 1123 1137 44.0 0.2093 2.3012 0.1530
> 1137 1138 86.5 0.1271 0.6245 0.1230
> 1137 1139 154.1 0.1377 0.5616 0.1330
> 2720 2721 35.4 0.1090 0.1090 0.1090
> Segmentation fault
>
> and my *.mdp file was:
>
> ;
> ; User spoel (236)
> ; Wed Nov 3 17:12:44 1993
> ; Input file
> ;
> cpp = cpp
> define = -DPOSRES
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 250000 ; total 10 ps.
> nstcomm = 1
> nstxout = 250
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 5
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 1.4
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = berendsen
> tc-grps = Protein SOL NA+
> tau_t = 0.1 0.1 0.1
> ref_t = 300 300 300
> ; Pressure coupling is on
> Pcoupl = berendsen
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
>
>
>
> Jahanshah Ashkani,
> PhD student of Biotechnology & Genetics,
> University of the Western Cape,
> Biotechnology Department,
> Private Bag X17,
> 7735 Bellville,
> Cape Town,
> South Africa
> jashkani at mail.biotech.uwc.ac.za
>
> ----- Original Message ----
>From: Justin A. Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Tuesday, December 4, 2007 7:27:35 AM
> Subject: Re: [gmx-users] Segmentation fault
>
>
> Quoting jahanshah ashkani <ashkani_2003 at yahoo.com>:
>
>> Hi,
>> I have got a segmentation fault error when I run mdrun for 1ns. I
> would be
>> glad if you let me know what is going on and how can I solve it.
>> Thank you very much.
>
> What happened before the segmentation fault?
>
> -Justin
>
>>
>> Best,
>>
>>
>> Jahanshah Ashkani,
>> PhD student of Biotechnology & Genetics,
>> University of the Western Cape,
>> Biotechnology Department,
>> Private Bag X17,
>> 7735 Bellville,
>> Cape Town,
>> South Africa
>> jashkani at mail.biotech.uwc.ac.za
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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