[gmx-users] topology problems

[Marc Bruning]

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??

regards,
marc