[gmx-users] About Warnings and Note in Production MD

[vidhya sankar]

Dear Justin Thank you for previous reply.
                                                                          I am doing Carbon nano tubes Wrapped by Cyclic peptide
After 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

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
step 141: Water molecule starting at atom 106721 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault


So I Have reduced the Time step Again I have received the same error as follows but this time 

Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault


How to Avoid Should I Equilibrate for Longer  time?  . I Have done 2ns Equilibration Only
Is My equilibration is not enough?

Thanks In Advance