[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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