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Good afternoon,<br>
<br>
I'm using GROMACS version 4.0.5. My simulation system is a double
stranded DNA (51 nucleotides) in a water (TIPI3P type) box, defined
as 0.9 A from the DNA, with 100 Na ions to neutralize the system.
The sequencial commands used were:<br>
<br>
1) pdb2gmx -f dsDNA.pdb -p dsDNA.top -o dsDNA.gro -ffamber99<br>
<br>
2) editconf -f dsDNA.gro -o box.gro -d 0.9<br>
<br>
3) genbox -cp box.gro -cs ffamber_tip3p.gro -o water.gro -p
dsDNA.top<br>
<br>
4) grompp -f em.mdp -c water.gro -p dsDNA.top -o Premin.tpr<br>
<br>
5) genion -s Premin.tpr -o water-ions.gro -np 100<br>
<br>
6) grompp -f em.mdp -c water-ions.gro -p dsDNA.top -o minIons.tpr<br>
<br>
7) MINIMIZATION: mdrun -v -s minIons.tpr -o minIons_traj.trr -x
minIons_traj.xtc -c minIons_final.gro -e minIons_ener.edr<br>
<br>
<br>
The problem appears when I try to minimize the system. When I try to
parallellize the calculation, the calculation returns with an error
message as follows: <br>
<br>
<i>Fatal error:<br>
There is no domain decomposition for 8 nodes that is compatible
with the given box and a minimum cell size of 38.1122 nm<br>
Change the number of nodes or mdrun option -rdd<br>
Look in the log file for details on the domain decomposition</i><br>
<br>
According to your web page, this error appears when a very small
system is too small to run parallellized. But my system is
extremelly big!! In previous calcs I could parallellize smaller
systems, even with just 8 nucleotides. <br>
I attach you the error file and the log file, as well as the mdp.<br>
I would be gratefull with any help. Thanks in advance,<br>
<br>
<br>
<br>
Núria Alegret<br>
University Rovira i Virgili - Tarragona (Spain)<br>
<br>
<br>
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