JMandumpal wrote:
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?
This is the same kind of error message as the one discussed here:
http://wiki.gromacs.org/index.php/Errors#LINCS_warnings and there's some
advice there.
Mark
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