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
>
>
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Received on Fri Apr 06 2012 - 23:00:02 PDT
