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