[gmx-users] Error There is no domain decomposition for 6 nodes that is compatible
sm.aguilera37 at uniandes.edu.co
Thu Oct 4 22:54:04 CEST 2012
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:
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.
Thank you in advance,
Universidad de los Andes-Colombia
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