[gmx-users] lost particles wile sorting

[Ming Tang]

Dear gromacs experts,

I am using semiisotropic coupling to pull a helix along z. I defined  wall like this:

pbc              =  xy
nwall            =  2
wall-atomtype    =  CH3 CH3
wall-type        =  12-6
wall-r-linpot    =  1 1
wall-density     =  5 5

But mdrun give me the following error:

Program mdrun, VERSION 5.0.4
Source code file: /home/tm/Downloads/gromacs/src/gromacs/mdlib/nbnxn_search.c, line: 737

Software inconsistency error:
Lost particles while sorting
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Then I tried to use 1 and 2 openMP threads, mdrun give me this error:

step 0: Water molecule starting at atom 40708 cannot be settled.
Check for bad contacts and/or reduce the time step if appropriate.

Segmentation fault (core dumped)

Could you please help to tell me how to fix this problem?

Thanks in advance.