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Dear all,<br><br>I am trying to do an md simulation of a system consiting of water and liquid crystalline molecules, starting from a random initial configuration.<br>After some energy minimization if I try to do an NVT simulation (I use the VERSION 4.0.3) I get the error <br><br>t = 0.000 ps: Water molecule starting at atom 8728 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br>step 0<br>Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)<br>Failing at addr:0x1005feee0<br>[0] func:/usr/lib64/openmpi/libopal.so.0 [0x3262d21dc5]<br>[1] func:/lib64/tls/libpthread.so.0 [0x326360c4f0]<br>[2] func:mdrun(gmx_pme_do+0x16b8) [0x4ba1c8]<br>[3] func:mdrun(do_force_lowlevel+0x118a) [0x48f1da]<br>[4] func:mdrun(do_force+0xdbd) [0x4cb51d]<br>[5] func:mdrun(do_md+0x31fa) [0x4328aa]<br>[6] func:mdrun(mdrunner+0x8ad) [0x42eb9d]<br>[7] func:mdrun(main+0x3e5) [0x435095]<br>[8] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3262f1c3fb]<br>[9] func:mdrun [0x41a29a]<br>*** End of error message ***<br>Segmentation fault<br><br>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.<br>Attached you can find my mdp file.<br>Any ideas?<br><br>Thanks<br>Antonia<br><br><br /><hr />check out the rest of the Windows Live™.
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