[gmx-users] step.pdb files during EM

JMandumpal jesbman at rediffmail.com
Tue Mar 4 07:23:12 CET 2008

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,
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