[gmx-users] nvt wouldn't run even after fixing the pdb file

[MD]

Hi Gromacs folks,

I was having problems running nvt which gave complaints about non-stable
system. I have tried minimizing structure at the first place, fixing broken
residues, using an alternate structure from pdb (same sequence, ) to start
with but I kept getting the either the same errors as following or
complaining about non settled water. I have googled and a lot of other
users solved the problem by minimizing the initial energy and fixing the
initial structure of pdb files but I have done both and it still wouldn't
work. I copied the messages after the mdrun nvt as following. Any help
would be appreciated.

Thanks,

Ming

gmx mdrun -deffnm nvt

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007935, max 0.215270 (between atoms 4621 and 4623)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.006332, max 0.171341 (between atoms 4621 and 4623)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4621   4623   30.8    0.1738   0.1675      0.1430
starting mdrun 'PROTEIN KINASE C in water'
50000 steps,    100.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.014407, max 0.495572 (between atoms 4628 and 4630)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4597   4599   39.4    0.1511   0.1596      0.1345
   4599   4600   32.7    0.1033   0.1027      0.0997
   4628   4630   34.6    0.1686   0.2139      0.1430
   4630   4631   34.8    0.1125   0.1189      0.1080
   4630   4632   35.9    0.1622   0.1875      0.1538
   4630   4643   60.7    0.1648   0.2089      0.1490
   4643   4644   48.5    0.1263   0.1176      0.1230
   4643   4645   67.1    0.1421   0.1584      0.1300

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.009036, max 0.242983 (between atoms 4619 and 4621)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4619   4620   32.6    0.1180   0.1435      0.1230
   4623   4626   33.2    0.1741   0.1794      0.1490
   4626   4627   36.2    0.1159   0.1417      0.1230
   4630   4631   59.2    0.1189   0.1326      0.1080

Step 2, time 0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005815, max 0.136241 (between atoms 4630 and 4631)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4628   4629   31.9    0.1022   0.1010      0.0997
   4630   4631   88.9    0.1326   0.1227      0.1080
   4630   4643   32.0    0.1627   0.1588      0.1490
   4643   4644   33.0    0.1269   0.1354      0.1230
   4643   4645   35.7    0.1405   0.1469      0.1300

Step 3, time 0.006 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.515541, max 37.148800 (between atoms 4630 and 4631)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4628   4629   84.6    0.1010   0.0676      0.0997
   4628   4630   76.9    0.1545   0.0962      0.1430
   4630   4631   89.7    0.1227   4.1201      0.1080
   4630   4643   38.3    0.1588   0.3132      0.1490
......
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 4626 and 4631
at distance 4.033 which is larger than the table limit 2.431 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



Step 4, time 0.008 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 5215.553278, max 375898.343750 (between atoms 4649 and 4650)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    199    200   37.9    0.1111   0.1110      0.1111
   4599   4600   36.0    0.0951   0.1413      0.0997
   4599   4601   30.4    0.1522   0.1079      0.1430
   4619   4620   34.1    0.1265   0.1685      0.1230
   4619   4621   39.3    0.1402   0.0512      0.1345
   4621   4622   54.5    0.1001   0.0990      0.0997
 ......
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)