[gmx-users] Genion failing in parallel runs.

[Florian Haberl]

Hi,

On Tuesday, 26. August 2008, Bhanu wrote:
> Hi,
> I'm using Gromacs 3.3.3, installed with double precision. When I run genion
> with this command:
>
> genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral
>
> the following error message was generated:
> ------------------------------------------------------------------------
>
> Program genion_d Version 3.3.3
> sourcecode file: init.c, line 69
>
> Fatal error:
> run input file prakash.tpr was made for 32 nodes
> while genion_d expected it to be for 1 node
> ---------------------------------------------------------------------------

use grompp without the '-np 32' option which defines the number of nodes. 
Genion runs on one node.

After neutralization you have to run grompp again, than also with '-np 32' 
option.


>---
>
> System is "protein in water", dodecahedron box. Everything is fine till
> energy minimisation. genion is failing.
>
> Any clue??
>
> Thanks.

greetings,

Florian


-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
-------------------------------------------------------------------------------