[gmx-users] mdrun

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Nov 14 15:37:51 CET 2009

Run some more energy minimization (EM). Make sure that you have  
constraints=none during EM (or I believe that you could also increase  
the LINCS/SHAKE iterations to the appropriate number). Also, while  
some people disagree in principle with me here, I also find in  
practice that a preliminary EM with define=-DFLEXIBLE (or otherwise  
depending on your water model) will help in some cases. If your EM is  
always stopping after 15 steps with max force=inf, then you need to go  
back to some of your previous setup steps and do them again while  
being a little more fastidious about the details (e.g. is your box  
size appropriate for your coordinates).

that error is telling you about what happened *at* 0.005 ps (t is not  
equal to dt).

Next time you post, please provide more information about how you set  
up and EM'd your system. Also, a better title gets better assistance.


-- original message --


I did command (mdrun -s -o -c -e -g) but following error was came up where
as my dt is 0.001 ps in mdp file:

t = 0.005 ps: Water molecule starting at atom 20937 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates.

I reduced time step but same error was came up again.I enlarged box size but
same error was came up again.

please guide me.

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