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

========================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to