[gmx-users] gromacs query

[Justin A. Lemkul]

Anushree Tripathi wrote:
> I m using gromacs 4.5.3 version and trying to simulate a protein in 
> liquid media but I found problem in eqilibration step especially when I 
> give following command:
> 
> mdrun -deffnm nvt
> 
> .After giving this command it is showing error,i.e.,
> There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 9.02659 nm
> Change the number of nodes or mdrun option -rdd or -dds
> 
> Look in the log file for details on the domain decomposition.
> What should I do now.Please suggest me.I tried above options also.
> 
> 

I don't see any reason why a normal protein in water simulation should require 
such a huge minimum cell size.  See here for more:

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

Likely you have something wrong in the topology, .mdp file, or both.

-Justin

-- 
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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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