[gmx-users] mdrun error

[pragya chohan]

hi i am trying to run mdrun for protein in membrane system. When i run mdrun i get a warning

Step -2, time -0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 2.144082 (between atoms 12433 and 12434) rms 0.216090
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  11761  11762   90.0    0.1633   0.2387      0.1000
  11929  11930   31.7    0.1633   0.1000      0.1000
  12097  12098   90.0    0.1632   0.1041      0.1000
  12265  12266   90.0    0.1633   0.2266      0.1000
  12433  12434   90.0    0.1633   0.3144      0.1000
starting mdrun 'alamethicin in popc'
500 steps,      0.5 ps.

Warning: 1-4 interaction between 115 and 136 at distance 1.144 which is larger t
han the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 12007 and 12008) rms inf
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  11619  11620   90.0    0.1000   0.1411      0.1000
  11633  11634   90.0    0.1000 13155507200.0000      0.1000
  11640  11641   90.0    0.1000   0.1214      0.1000
.....
  12619  12620   90.0    0.1080   0.1447      0.1080
Wrote pdb files with previous and current coordinates
step 0Segmentation fault
I am using shake in my mdp file. I want to restrain water.

my mdp file is:
title                = popc128a
integrator           = md
define               = -DFLEX_SPC
dt                   = 0.001
nsteps               = 500
nstxout              = 500
ns_type              = grid
pbc                  = xyz
constraints          = hbonds
constraints_algorithm= shake
coulombtype          = PME
vdwtype              = cut-off
rcoloumb             = 1.0
nstlist              = 10.0
Tcoupl               = no
pcoupl               = no
compressibility      = 4.5e-5
gen_temp             = 300
gen_vel              = no
Please help.
Thanks in advance.
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