[gmx-users] Change in .gro in grompp

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 6 22:30:13 CET 2008

Caleb Carlin wrote:
> First, thank you to everyone that responded.  The suggestions for 
> viewing the output of grompp worked.
> Grompp was changing the configuration file because of the order of the 
> molecules in the .top file.  The initial .gro file listed the silicon 
> first and the water second, while the .top listed them the other way 
> around.  Reversing these in the [molecules] section resolved the issue.  
> The ordering in the itp file may have affected this as well.

Atom ordering within molecules needs to correspond between structure 
file and topology file, and order of molecules in the [ molecules ] 
section also needs to correspond. I've just looked in Chapter 5 of the 
manual and can't find anywhere that specifies this, and it should be 
there. Any ideas, people?

> The symptoms were a reordering of atoms in the .gro file and the 
> following error in the grompp output:
> Warning: atom names in topol.top and Config.GRO don't
>> match (O - SI)

Ah, some useful information. Telling the people you're asking for help 
about the warning messages you were getting would have been a way to get 
your problem solved more quickly using less of their time.


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