[gmx-users] grompp -shuffle causes unsettled water error during mpirun C mdrun (but not using -shuffle completes mpirun C mdrun)

Sabuj Pattanayek sabuj.pattanayek at vanderbilt.edu
Tue Mar 22 19:32:15 CET 2005


I'm running mdrun across 3 nodes using lam-mpi v7.0.6 + gromacs v3.2.1. 
Whenever I use grompp -shuffle and then do mpirun C mdrun I get an error 
like this:

t = 0.004 ps: Water molecule starting at atom 4324 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates

Usually if there truly is an error with my input, mdrun proceeds to dump 
out long bonds that violate LINCS contraints and bonds that rotated more 
than 30 deg, but in this case there are no outputs.

If I do not use grompp -shuffle then the run proceeds without any errors.

Any ideas why this may be occurring?

Sabuj Pattanayek

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