On Tue, 27 Sep 2016 11:08:45 +0100
Rui Neves <rppne...@gmail.com> wrote:
> However, what I would like to know is:
> At the beggining of the topology I call for all the bonded terms
> ('#include ffbonded.itp), and then in the [ atoms ] section, I
> specify the massB, typeB and chargeB for the B-state. Do I have to
> explicitly write the parameters for the B-state of the [ bonds ],
> [ angles ] and [ dihedrals ] section, or are they read from the
> ffbonded.itp file, since I have defined the typeB for the atoms in
> the B-state?
If you wish to have the same parameters (for non-changing bonded terms)
there is not need to fill in the B state. However, if the bonded
parameters change, your topology file will necessarily have to reflect
this and you need to change the B state accordingly. Grompp doesn't
make any assumption as to what you want esp. in the case of
disappearing/appearing atoms (where the typically approach is to take
the parameters from the other state i.e. the one where the bonded term
exists). For torsions Gromacs would require a term-by-term matching
(same periodicities).
Cheers,
Hannes.
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