[gmx-users] NPT equillabration Error bilayer

[MRINAL ARANDHARA]

I am trying to run a lipid bilayer simulation but during the npt equillibration step I am getting the following error
"1 particles communicated to PME rank 6 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y"
I have successfully run the NVT equillibration.What may be the  problem??
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step 52083: Water molecule starting at atom 197027 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 52083: Water molecule starting at atom 197027 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

step 52085: Water molecule starting at atom 197027 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 52085: Water molecule starting at atom 197027 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
^Mstep 52100, will finish Wed Mar  8 18:13:02 2017
step 52123: Water molecule starting at atom 197027 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 52123: Water molecule starting at atom 197027 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

step 52126: Water molecule starting at atom 197027 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 52126: Water molecule starting at atom 369101 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

-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.4
Source code file: /nishome/mishra/gromacs-5.1.4/src/gromacs/ewald/pme-redistribute.cpp, line: 276

Fatal error:
@1 particles communicated to PME rank 6 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS                                                                                                                      
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