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