[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:
> I make the solution box of organic solvent. It is homeogen and mixed
> 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.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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