[gmx-users] step.pdb files during EM

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 4 08:57:29 CET 2008

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.


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