[gmx-users] Segmentation fault
jahanshah ashkani
ashkani_2003 at yahoo.com
Sat Dec 29 06:17:10 CET 2007
Hi,
I am using a Mac version of GROMACS and my Mac is a MacBook (Intel Core Duo) with following characteristics:
Processor Speed: 2 GHz
Number Of Processors: 1
Total Number Of Cores: 2
L2 Cache (per processor): 2 MB
Memory: 2 GB
Bus Speed: 667 MHz
I have got a segmentation error while mdrun is running for my protein with two chains (A & B).
I would be glad if somebody help me in this case.
Thank you very much.
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: Xinghua Shi <xinghua.shi at gmail.com>
To: gmx-users at gromacs.org
Sent: Saturday, December 29, 2007 2:49:51 AM
Subject: [gmx-users] modify the Lennard Jones potential
Hi guys,
I want to modify the Lennard Jones potential, i.e. to add some term in
this equation. I wonder if anyone know which source file should I
modify.
Best regards
Xinghua
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