[gmx-users] No domain decomposition

[soumadwip ghosh]

Thanks Tsjerk for your help. But I started the mdrun using the command
mdrun -deffnm em -nt 8 and it gave the following outcomes.

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Warning: 1-4 interaction between 1544 and 1554 at distance 3.261 which is
larger than the 1-4 table size 2.000 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
or with user tables increase the table size

step 31: Water molecule starting at atom 63649 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

step 34: Water molecule starting at atom 46552 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

step 35: Water molecule starting at atom 46552 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

step 37: Water molecule starting at atom 64213 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

step 38: Water molecule starting at atom 46045 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 1568 steps
Potential Energy  = -1.7034508e+06
Maximum force     =  9.5823822e+02 on atom 1546
Norm of force     =  1.3556979e+01

As you can see the files have been created but I get the above warnings
hinting at the system blowing up. I have taken the em.gro file and did an
NVT for 100 ps with 0.001 timestep and it resulted is segmentation faults
as below.

step 675: Water molecule starting at atom 43849 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 (core dumped)

What should I do? Was the command used for mdrun ( -nt 8) wrong? Am I
missing something important. Your help will be appreciated.

Thanks and regards,
Soumadwip Ghosh
Research Fellow
IITB
Mumbai
India