[gmx-users] system couldn't be run

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 12 14:36:30 CEST 2008

Morteza Khabiri wrote:
> Dear
> I make the solution box of organic solvent. It is homeogen and mixed
> properly.
> It also has a minimum energy. I put one protein in this solution. Before
> put the protein in the solution I minimimized it also. Now I mixed 2
> system which each of them are minimized. After put the protein in the
> solution I try first to minimized it then run it but unfortunately it
> crashed. I did not work at all. I also tried to run the system without
> minimization but it also did not work at all. I changed mdp file (

If the system crashes during minimization, I certainly wouldn't expect it to do 
anything but crash if you don't run EM!

> eg,remove center of mass motion or decrease the temprature,..) but non of
> them did work.

Usually it is better to show the .mdp file than to make us guess at what you've 

> Thats very nice of you if you guid me what should i do?

Dealing with mixed solvents can be difficult.  You probably have some severe 
overlap that cannot be resolved by energy minimization.  Usually if you set 
nstxout = 1 in the .mdp file you can get a glimpse of where the system begins to 
explode.  That will provide some clues.


> Thanks
> Morteza
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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