Sorry for not using the right terminology . I have used explicit solvent
simulations.
I want to calculate the change in solvation free energy of polymer in
presence of ions.
Is this only for implicit solvent models.
Thanks
Kirtana
On Sat, Apr 7, 2012 at 1:55 AM, Aron Broom <broomsday.gmail.com> wrote:
> I'm not totally clear on what you want to measure, do you want to measure
> the binding energy for a SINGLE water molecular to your UNSOLVATED polymer
> in a vacuum? MMPBSA is generally used with implicit solvent, but if you
> want to use the same method and just mimic being in a vacuum, you can set
> the external dielectric to 1.0, it's not the most efficient method, but it
> should work.
>
> ~Aron
>
> On Sat, Apr 7, 2012 at 1:35 AM, kirtana S <skirtana4.gmail.com> wrote:
>
> > I want to calculate the binding of water molecules with the polymer
> chains
> > in presence of ions and compare my results to another system without the
> > presence of ions.
> > Is there any utility which can help in the calculations
> >
> > Thanks
> > Kirtana
> > On Fri, Apr 6, 2012 at 9:04 PM, case <case.biomaps.rutgers.edu> wrote:
> >
> > > On Fri, Apr 06, 2012, kirtana S wrote:
> > > >
> > > > My system consists of a polymer molecule in explicit water(TIP3P)
> with
> > > > ions. Using MMGBSA I have to use a vacuum trajectory and topology
> files
> > > of
> > > > each ligand and receptor.
> > > > Now to calculate the binding free energy of solvent with the polymer
> > > > molecule how should I go about.
> > >
> > > It's not clear what energy you want: there would not ordinarily be a
> > > "binding
> > > free energy" between a polymer and solvent. Or at least, you would
> have
> > to
> > > define this carefully.
> > >
> > > One could estimate the transfer free energy between gas phase and
> water,
> > > which
> > > would be something like a free energy of interaction between the two.
> > But
> > > this
> > > is not often an interesting value per se, since it generally can't be
> > > measured.
> > >
> > > ....dac
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 07 2012 - 12:00:02 PDT
