[gmx-users] md error message

[Mark Abraham]

Antonia V. wrote:
> Dear all,
> 
> I am trying to do an md simulation of a system consiting of water and 
> liquid crystalline molecules, starting from a random initial configuration.
> After some energy minimization if I try to do an NVT simulation (I use 
> the VERSION 4.0.3) I get the error

Please update to 4.0.4.

> t = 0.000 ps: Water molecule starting at atom 8728 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> step 0

See http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings

Mark

> Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
> Failing at addr:0x1005feee0
> [0] func:/usr/lib64/openmpi/libopal.so.0 [0x3262d21dc5]
> [1] func:/lib64/tls/libpthread.so.0 [0x326360c4f0]
> [2] func:mdrun(gmx_pme_do+0x16b8) [0x4ba1c8]
> [3] func:mdrun(do_force_lowlevel+0x118a) [0x48f1da]
> [4] func:mdrun(do_force+0xdbd) [0x4cb51d]
> [5] func:mdrun(do_md+0x31fa) [0x4328aa]
> [6] func:mdrun(mdrunner+0x8ad) [0x42eb9d]
> [7] func:mdrun(main+0x3e5) [0x435095]
> [8] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3262f1c3fb]
> [9] func:mdrun [0x41a29a]
> *** End of error message ***
> Segmentation fault
> 
> The time step I am using is 0.002, but even when I try a smaller  one I 
> get the same error. The water molecules are not flexible and I am not 
> using any constraints for the LC.
> Attached you can find my mdp file.