[gmx-users] genion on a dual machine

vechism at netscape.net vechism at netscape.net
Thu Sep 22 20:24:50 CEST 2005

Hi All,

I was used to running gromacs on a single node and now I'm using it on dual opteron machine and I'm having problems using genion this machine.

First I ran,
pdb2gmx -ff G43a1 -f mol.pdb -p mol.top -i mol.itp -o mol.gro
editconf -bt cubic -d 1.2 -f mol.gro -o out.gro
genbox -cp out.gro -cs -p mol.top -o b4em.gro
grompp -np 2 -v -f em_mol.mdp -c b4em.gro -o em.tpr -p mol.top

Then I ran,

genion -np 3 -pname NA+ -pq 1 -s em.tpr -o na_ion_1_added.gro -g genion.log

and I got this error:

WARNING: turning of free energy, will use lambda=0
Reading file em.tpr, VERSION 3.2.1 (single precision)
Fatal error: run input file em.tpr was made for 2 nodes,
             while genion expected it to be for 1 nodes.

How can I tell to genion to use 2 nodes? Or ... Should I use genion before grompp?

Thanks in advance.


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