[gmx-users] gromacs error

[Urszula Uciechowska]

Dear Gromacs users,


I tried to run coarse grained MD however after a few steps I got:
Step 39, time 0.78 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.038933, max 2.260527 (between atoms 10459 and 10463)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  10457  10459   89.8    0.3107   0.8288      0.3100
  10459  10463   90.3    0.3075   1.0108      0.3100
  10463  10467   90.6    0.3084   0.8774      0.3100
  10467  10469   81.1    0.3103   0.3823      0.3100
  10469  10471   90.3    0.3121   0.1885      0.3100
Wrote pdb files with previous and current coordinates

Step 40, time 0.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 165002.767686, max 10334958.000000 (between atoms 10457 and 10459)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  10443  10445   30.1    0.3100   0.3581      0.3100
  10445  10447  102.2    0.3102 266.6146      0.3100
  10447  10450   59.3    0.3100 624.1382      0.3100
  10450  10452  101.4    0.3105 5390.4609      0.3100
  10452  10454   87.9    0.3083 104154.3047      0.3100
  10454  10457   83.9    0.3497 439143.5312      0.3100
  10457  10459   87.5    0.8288 3203837.2500      0.3100
  10459  10463   87.8    1.0108 2960821.2500      0.3100
  10463  10467   95.2    0.8774 763857.8125      0.3100
  10467  10469   95.5    0.3823 195859.2656      0.3100
  10469  10471  104.3    0.1885 43565.4141      0.3100
  10471  10473   90.3    0.3534 7857.3394      0.3100
  10473  10475  105.5    0.3125  57.7529      0.3100
  10475  10477   90.0    0.3099   0.3849      0.3100
  10477  10480   32.4    0.3101   0.3647      0.3100
Wrote pdb files with previous and current coordinates
mpiexec: process_obit_event: evt 6 task 0 on wn518 stat 267.
mpiexec: wait_tasks: waiting for wn350 wn350 wn501.
mpiexec: kill_others_now: alarm went off, killing all other tasks.
mpiexec: kill_tasks: killing all tasks.
mpiexec: process_kill_event: evt 10 task 1 on wn350.
mpiexec: process_kill_event: evt 12 task 3 on wn501.
mpiexec: process_kill_event: evt 11 task 2 on wn350.
mpiexec: process_obit_event: evt 7 task 3 on wn501 stat 265.
mpiexec: process_obit_event: evt 8 task 1 on wn350 stat 265.
mpiexec: process_obit_event: evt 9 task 2 on wn350 stat 265.
mpiexec: Warning: task 0 died with signal 11 (Segmentation fault).
mpiexec: Warning: tasks 1-3 died with signal 9 (Killed).

in log file last line is:

Constraining the starting coordinates (step 0)

Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 4.04e-06
Initial temperature: 1.8161e-07 K

Started mdrun on node 0 Wed Jul 30 10:39:50 2014

           Step           Time         Lambda
              0        0.00000        0.00000

Grid: 42 x 42 x 42 cells
   Energies (kJ/mol)
           Bond       G96Angle    Proper Dih.  Improper Dih.        LJ (SR)
    6.24872e+03    1.47844e+04    1.75778e+03    4.11810e+02   -2.32179e+07
   Coulomb (SR) Position Rest.      Potential    Kinetic En.   Total Energy
   -4.49776e+03    2.00073e-01   -2.31992e+07    1.44043e+01   -2.31992e+07
    Temperature Pressure (bar)   Constr. rmsd
    1.55259e-03   -1.41563e+03    5.56533e-06

my input file:

define           =  -DPOSRES
dt               =  0.02
nsteps           =  25000
nstxout          =  0
nstvout          =  0
nstlog           =  100
nstxtcout        =  100
xtc-precision    =  10
rlist            =  1.4
coulombtype      =  shift
rcoulomb         =  1.2
epsilon_r        =  15
vdw-type         =  shift
rvdw-switch      =  0.9
rvdw             =  1.2
tcoupl           =  v-rescale
tc-grps          =  Protein W
tau-t            =  1.0 1.0
ref-t            =  300 300
Pcoupl           =  Berendsen
Pcoupltype       =  isotropic
tau-p            =  12.0
compressibility  =  3e-4
ref-p            =  1.0
refcoord_scaling =  com

What is wrong here?

best regards
Urszula Uciechowska


-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/