[gmx-users] query against box collapsed in case of tightly bound ligand

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 26 13:47:16 CET 2011

devawati dutta wrote:
> Dear Sir,
>                  Thank you for your suggestion regarding coulomb type 
> and LIE method. I have successfully done the job. But now I am facing 
> another type of problem. I am performing
>                  simulation of a protein ligand complex where the ligand 
> is sitting deep inside the grrove of the protein. When  I have done the 
> molecular dynamic simulation , its
>                  showing an error as : Number of grid cells is zero. 
> probably the system and the box collpased. I have searched through the 
> mailing list, but I failed to get a proper
>                  answer. I have run the simulation in discovery studio 
> and the simulation was successfully done.Please suggest me in this regard.

Possible reasons and diagnostic tips can be found here:


If you want more detailed help, you will have to provide (at least):

1. A description of your EM and equilibration procedure
2. The topology for your ligand and how you generated it
3. The .mdp file of the run that crashed


> Your's sincerely
> Devawati Dutta


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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