[gmx-users] Error There is no domain decomposition for 6 nodes that is compatible
jalemkul at vt.edu
Thu Oct 4 22:59:04 CEST 2012
On 10/4/12 4:54 PM, Sonia Aguilera wrote:
> I am performing a free energy calculation based on Justin Lemkul's tutorial.
> My system is a protein in water and dodecane and I'm coupling the protein
> considering none to only vdw interactions for my lambda 0 and 1 states.
> However, I get this error when trying to minimize the system:
> Fatal error:
> There is no domain decomposition for 6 nodes that is compatible with the
> given box and a minimum cell size of 7.55833 nm min1.0.mdp
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> I know I can fix easily this problem by using -nt 1 option. But I still want
> to use all available cores. I suspect the error is in the mdp file because
> if I use the following mdp file for the minimization it works.
> title = cpeptide
> cpp = /usr/bin/cpp
> define = -DFLEX_SPC
> constraints = none
> integrator = steep
> dt = 0.002 ; ps !
> nsteps = 1000
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.0
> ; Energy minimizing stuff
> emtol = 1000.0
> emstep = 0.01
> Obviously this mdp file does not work for free energy calculations. I still
> want to use the attached one, but I don´t know what to change to make it
> This is the link for my log and mdp file.
The problem comes from these settings:
couple-moltype = Protein_chain_A ; name of moleculetype to decouple
couple-lambda0 = none ; turn off everything
couple-lambda1 = vdw ; only van der Waals interactions
couple-intramol = no
You're transforming the protein using long-range exclusions and pair
interactions (couple-intramol = no). These interactions make the required DD
cell size very large. Then you run into the fact that you can't decompose any
system into any arbitrary number of DD cells, because their size is limited by
the bonded interactions, pairs, cutoffs, and other factors.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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