Dear list,
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.
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.
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".
I constructed the water box using packmol
program. If I want to avoid these error messages, What should I do?
thanks in advance,
Jestin
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