[gmx-users] md error message

Antonia V. antonia_haha at hotmail.com
Thu Apr 30 11:48:09 CEST 2009

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 

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
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.
Any ideas?


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