[gmx-users] genion on a dual machine

[David]

On Thu, 2005-09-22 at 14:24 -0400, vechism at netscape.net wrote:
> 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?
make a 1 processor tpr file.

> 
> Thanks in advance.
> 
> 
> Sergio.
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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