[gmx-users] Re: Atom names mismatch

[George Abadir]

Hi,
     Thank you for your reply. It is a grompp error not an mdrun error 
as you say. I read the manual entry. What I don't understand is: does 
grompp first change the atom names and then assigns the atom type at the 
specific coordinate according to the new name, ordoes  it assign the 
atom type according to the coordinate file and then uses the atom name 
corresponding to the atom type.
     Thank you very much,
Regards,
George

Low Soo Mei wrote:

> Hi,
>
> Perhaps I am overlooking something very obvious in this, but was this 
> really a log file (mdrun) error or a grompp error?
>
> Manual entry for grompp says "grompp uses the atom names from the 
> topology file. The atom names in the coordinate file (option -c) are 
> only read to generate warnings when they do not match the atom names 
> in the topology. Note that the atom names are irrelevant for the 
> simulation as only the atom types are used for generating interaction 
> parameters."
>
> Cheers,
> Soo Mei
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