Chih-Ying Lin wrote:
Hi
After the two commands,
grompp_mpi -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr
mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-vacuum
Fatal error:
pbc type no is not supported with domain decomposition,
use particle decomposition: mdrun -pd
What does it mean?
The message is quite clear - you cannot use "pbc = no" with domain decomposition
(explained in the manual and the Gromacs 4 paper). You have to revert to using
particle decomposition with -pd in order to use "pbc = no."
-Justin
Thank you
Lin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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