[gmx-users] topology problems

[Anton Feenstra]

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?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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