There are various different types of monomers such as acetic acid,
pyridine, benzene etc. They can be kept rigid by doing ntr = 1 and applying
a large force constant to the required residues (usually just the first
two).
Sanmeet
On Tue, Mar 17, 2015 at 7:25 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> what are the monomers? how difficult will it be to keep them rigid?
>
> On Tue, Mar 17, 2015 at 5:18 PM, Sanmeet Chahal <schah063.uottawa.ca>
> wrote:
>
> > Hello All,
> >
> > I need to compute a PMF for the dissociation of a dimer in TIP3P water. I
> > need each dimer to remain 'rigid' from an intramolecular and relative
> > standpoint. My PMF transformation is simply moving only one monomer away
> > from the other monomer with a simple translation of their atoms. The goal
> > of this calculation is to mimic a PB-type PMF along the separation axis
> but
> > now with proper statistics and explicit solvent.
> >
> > I thought that thermodynamic integration would be the right formalism for
> > this in AMBER (though umbrella sampling could be more efficient).
> >
> > What is the best way to compute this PMF calculation in AMBER? Any
> example?
> >
> > Thanks,
> > Sanmeet
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Received on Tue Mar 17 2015 - 19:30:02 PDT
