[gmx-users] topology problems

[Marc Bruning]

> Did you use grompp -shuffle ?
>
> Do you use the same .gro file that you supplied to grompp?

hello,

actually i use grompp -shuffle -sort (+ mpirun on a cluster with 16 nodes). 
for the pr grompp command i use exactly the *.gro file as input that i get 
from the em mdrun command. before the em the order in the *.gro file is 
something like: protein, ligand1, ligand2, sol, na. afterwards it is like: 
protein, ligand1, sol, ligand2, sol, na, sol, na, sol etc.... it is rather 
easy to copy this new order into the *.top file, but why the ions are not 
recognized any more i do not understand at all.

regards,
marc

On Wednesday 28 July 2004 15:40, you wrote:
> Marc Bruning wrote:
> > dear users,
> >
> > after energy minimizing a protein together with two ligands using gromacs
> > the molecule order in the resulting *.gro file is different from the one
> > in the *.top file for the same protein. if i change the order of
> > molecules in the molecule section of the *.top file the system gets a non
> > zero charge again (i am using PME) and if i do not change the order,
> > 'grompp' mixes up the bonded atoms, leading to a crash of the LINCS
> > algorithm in the following pr-run. does anybody know, why this happens??
>
> Did you use grompp -shuffle ?
>
> Do you use the same .gro file that you supplied to grompp?

-- 
marc bruning 
mpg-asmb