[gmx-users] Using groups in the mdp file

Ignacio Fernández Galván jellby at yahoo.com
Thu Feb 9 18:03:39 CET 2012

--- On Mon, 6/2/12, Ignacio Fernández Galván <jellby at yahoo.com> wrote:

> The .gro file does not contain any mention to "ACX", but I
> believe it's not needed, as long as it's in the .top,
> right?

It seems that default group names are generated not from moleculetype names, but from residue names. At least that's what it says in http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx:

default index groups are already generated (entire system, 9 groups for proteins, and one for every other *residue name*).

In my case, if I use GLC (residue) for energygrps instead of ACX (molecule), it works fine.

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