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? Thanks Antonia _________________________________________________________________ More than messages–check out the rest of the Windows Live™. http://www.microsoft.com/windows/windowslive/
lc5cbNPT.mdp
Description: Binary data
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