[gmx-users] typeB in FEP calculations
rppneves at gmail.com
Fri Sep 30 18:56:22 CEST 2016
Thank you very much for your help.
I think that I finally got this straight.
On 27 September 2016 at 11:26, Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk>
> On Tue, 27 Sep 2016 11:08:45 +0100
> Rui Neves <rppneves at 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).
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users