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