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Dear list,<BR>
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I ran EM (energy minimisation) of TIP5P water model using gromacs/3.3.2 version. My output says : Steepest Descents converged to Fmax < 100 in 427 steps. Moreover, my output.gro file looks ok after the run. But in the directory, there were some files (8), called step.pdb, generated. <BR>
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But, it is said, actually simulation crashed, that is why these files are being generated ( Thread 2004 January). But in my case, if the program was crashed, then why it ran till 427th step to finish EM to the desired accuracy.<BR>
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Furthermore, when I inspected the output file, I found the following similar messages on 8 occasions : "t = 0.023 ps: Water molecule starting at atom 356 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates".<BR>
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I constructed the water box using packmol program. If I want to avoid these error messages, What should I do?<BR>
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thanks in advance,<BR>
Jestin<BR>
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