[gmx-users] grompp question: rest group created for unspecified constraints

David Mathog mathog at caltech.edu
Thu Feb 16 19:55:25 CET 2006

The demo script in gmxdemo doesn't specify anything for Tcoupl,
tau_t, tc-grps, or ref-t in em.mdp for the energy minimization step.
When grompp runs with this input file it triggers the creation
of a "rest" group in readir.c that seems to contain every last
atom in the model.  That happens for all of the other
constraints that might have been specified too.

If a constraint isn't specified why is a "rest" group needed?  

The output of grompp is very puzzling because it says, for instance:

making "rest" group for User1 containing 51332 elements:
User1        has 1 element(s):  rest

And so on for all of them (freeze, user2,xtc etc.)

1.  Should "element(s)" be "group(s)"?
2.  Why are groups created for constraints (T-Coupling etc.)
that were not specified?  The end user can't tell if grompp is
falling over to some default constraint or if it's just creating
a group it will never use.


David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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