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

[Justin A. Lemkul]

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:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

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

-Justin

>  
> Your's sincerely
> Devawati Dutta
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================