[gmx-users] grompp error
feenstra at chem.vu.nl
Thu Aug 5 09:21:20 CEST 2004
Steffen Haerterich wrote:
> Check if your Protein is named Protein in your topology of the
> Sometimes a chainidentifier may creep into the name. (e.g. Protein_X)
> You would then have to adjust the name within the topologie and/or
> mdp-file. I don't know if Gromacs is case-sensitive.
> I hope this is of any help .
This is not relevant. Molecule names are used within the topology, to
define the molecule and build the system consisting of molecules.
The group options grompp complains about, refer to the Index Groups,
as defined by default, or by your .ndx file.
While this may seem confusing, the reason is simple. By having the groups
(and group names) independent of molecule definitions (and names), one can
define groups consisting of many molecules, or even of part of one molecule.
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