On 6/11/12 4:37 AM, Seera Suryanarayana wrote:
Dear Justin sir,
I am simulating a protein 1AKI.pdb which is example of
your tutorial.I am doing simulations as your tutorial.I didnt get any errors
upto the commond "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o
em.tpr".After this as your tutorial i used the commond " mdrun -v -deffnm em",
then i got the following error.
Fatal error:
Domain decomposition does not support simple neighbor searching, use grid
searching or use particle decomposition
Kindly tell me how to overcome this error.
Mark has already addressed this issue:
http://lists.gromacs.org/pipermail/gmx-users/2012-June/072299.html
You will either need to make a suitable change to the .mdp file or to the mdrun
command line, both of which are suggested in the error message.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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