[gmx-users] About Production MD run error

[vidhya sankar]

Dear Justin Thank you for previous reply.
                                                                          I am doing Carbon nano tubes Wrapped by Cyclic peptide .I am sure of that iher is no error in My topology of My system (CNT Wrapped by Cyclic peptide) 
After Successful  NPT and NVT equilibration  When i Run Production MD I have got The following Notes in terminal

NOTE 1 [file CNTCYCfull.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy
NOTE 2 [file CNTCYCfull.mdp]:
  You are using a cut-off for VdW interactions with NVE, for good energy
  conservation use vdwtype = Shift (possibly with DispCorr)
NOTE 3 [file CNTCYCfull.mdp]:
  You are using a cut-off for electrostatics with NVE, for good energy
  conservation use coulombtype = PME-Switch or Reaction-Field-zero
NOTE 4 [file gfggZ.top, line 60]:
  For energy conservation with LINCS, lincs_iter should be 2 or larger.

if I ignore the Notes  I am Not Able to run . S I have Changed All options Accordingly in .mdp files Then
When I run I have got the following errors after few Minutes

step 100, will finish Thu Oct 10 18:44:32 2013
Step 153, time 0.0306 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.010047, max 0.158996 (between atoms 875 and 873)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

rms 37613.979597, max 954780.695847 (between atoms 1189 and 1190)
   1157   1156   34.0    0.0997   0.1118      0.1000
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1171   1158   36.4    0.1542   0.1972      0.1530
   1159   1158   34.8    0.1534   0.2022      0.1530
   1178   1176   67.6    0.1528   2.4354      0.1530
   1179   1177   79.1    0.1533   0.2981      0.1530
   1046   1044   35.1    0.1489   0.3847      0.1470
Fatal error:
3 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS

Thanks In Advance